PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments

Native domain record

NSD3 PWWP1

Histone-lysine N-methyltransferase NSD3

Q9BZ95 at UniProt
Homo sapiens1437 amino acidsannotation supportedUP:Q9BZ95:PWWP1
2annotated cores in NSD3
11PDB entries with observed PWWP1 coordinates
5model records for PWWP1
9frozen v1.2 assay / association records for PWWP1

Canonical sequence · Source-mapped regions

Protein domain architecture

1437 residues

PWWP annotation cores, other annotated regions, and deposited construct mappings share the canonical amino acid axis. The original Atlas PWWP intervals retain their source definitions.

PWWP annotation cores PWWP1 · 270–333 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket PWWP2 · 960–1022 · UniProtKB reviewed feature · annotation core; not a certified complete folded domain or pocket Other source annotations Zinc finger: PHD-type 1 · 701–748 · UniProtKB source annotation Zinc finger: PHD-type 2 · 749–805 · UniProtKB source annotation Zinc finger: PHD-type 3 · 862–955 · UniProtKB source annotation Domain: AWS · 1093–1143 · UniProtKB source annotation Domain: SET · 1145–1262 · UniProtKB source annotation Domain: Post-SET · 1269–1285 · UniProtKB source annotation Zinc finger: PHD-type 4; atypical · 1321–1368 · UniProtKB source annotation 1 359 718 1078 1437
PWWP annotation coreOther source annotationPredicted candidate, when present
7 additional source-supported regions · coordinates and evidence

UniProt feature coordinates accepted after exact canonical sequence identity check against the frozen Atlas. Source annotations can be inferred by sequence or curated from experiments; evidence codes remain attached. Other domain types link to their UniProt source because the Atlas records PWWP domains.

Source featureTypeAmino acidsEvidence
PHD-type 1Zinc finger701–748ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 2Zinc finger749–805ECO:0000255 PROSITE-ProRule: PRU00146
PHD-type 3Zinc finger862–955ECO:0000255 PROSITE-ProRule: PRU00146
AWSDomain1093–1143ECO:0000255 PROSITE-ProRule: PRU00562
SETDomain1145–1262ECO:0000255 PROSITE-ProRule: PRU00190
Post-SETDomain1269–1285ECO:0000255 PROSITE-ProRule: PRU00155
PHD-type 4; atypicalZinc finger1321–1368ECO:0000255 PROSITE-ProRule: PRU00146

Deposited construct mapping

4 selected examples

Colored segments map deposited polymer sequences to this canonical protein; dark segments have observed coordinates. Unmapped tags and engineered residues are not assigned canonical positions. These are not certified whole-fold boundaries.

6G25chain A263–398
Mapped deposited segment 263–398 Observed canonical residues 266–343Observed canonical residues 354–396
Mapping and construct evidence

Deposited polymer length: 136 residues. Mapped sequence identity: 100.0%. no sequence difference detected by mapping; not proof of wild type.

PWWP1: 64 / 64 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

4RXJchain A953–1064
Mapped deposited segment 953–1064 Observed canonical residues 957–1064
Mapping and construct evidence

Deposited polymer length: 113 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP2: 63 / 63 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

Unmapped construct positions: 1–1.

2DAQchain A957–1053
Mapped deposited segment 957–1053 Observed canonical residues 957–1053
Mapping and construct evidence

Deposited polymer length: 110 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP2: 63 / 63 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

Unmapped construct positions: 1–7, 105–110.

6G3Pchain A247–398
Mapped deposited segment 247–398 Observed canonical residues 249–256Observed canonical residues 264–343Observed canonical residues 360–395
Mapping and construct evidence

Deposited polymer length: 153 residues. Mapped sequence identity: 100.0%. sequence differences or tags detected; biological versus engineered origin requires review.

PWWP1: 64 / 64 annotation-core Cα residues observed.

Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.

Unmapped construct positions: 1–1.

One mapped example per native domain, preferring frozen experimental representatives; up to four distinct mapped intervals.

Validated isoform differences · 8 PWWP correspondence records

Only source-validated PWWP core correspondences from the frozen v1.2 isoform audit; other-domain architectures are not projected onto isoforms. Coordinates in the isoform column refer to the individual isoform sequence; deleted cores remain absent.

IsoformLengthPWWP coreSource-mapped positionsRetention / source edits
Q9BZ95-21388PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-21388PWWP2911–973
63 / 63 mapped residues; span may contain gaps		complete
Q9BZ95-3645PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-3645PWWP2Noneabsent
Q9BZ95-41374PWWP1207–270
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-41374PWWP2897–959
63 / 63 mapped residues; span may contain gaps		complete
Q9BZ95-51426PWWP1270–333
64 / 64 mapped residues; span may contain gaps		complete
Q9BZ95-51426PWWP2960–1022
63 / 63 mapped residues; span may contain gaps		complete
Viewing NSD3 PWWP1

Canonical annotation interval 270–333 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.

Alternative PWWP annotations and interval provenance
[
  {
    "end": 331,
    "identifier": "SM00293",
    "integrated_identifier": "IPR000313",
    "model": "SM00293",
    "name": "domain with conserved PWWP motif",
    "representative": false,
    "score": 1.7e-12,
    "source": "smart",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 268
  },
  {
    "end": 349,
    "identifier": "IPR000313",
    "integrated_identifier": null,
    "model": null,
    "name": "PWWP domain",
    "representative": false,
    "score": null,
    "source": "interpro",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 268
  },
  {
    "end": 397,
    "identifier": "IPR047451",
    "integrated_identifier": null,
    "model": null,
    "name": "Histone-lysine N-methyltransferase NSD3, first PWWP domain",
    "representative": false,
    "score": null,
    "source": "interpro",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 268
  },
  {
    "end": 397,
    "identifier": "cd20163",
    "integrated_identifier": "IPR047451",
    "model": "cd20163",
    "name": "first PWWP domain found in nuclear SET domain-containing protein 3 (NSD3) and similar proteins",
    "representative": false,
    "score": 1.673e-91,
    "source": "cdd",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 268
  },
  {
    "end": 333,
    "identifier": "PS50812",
    "integrated_identifier": "IPR000313",
    "model": "PS50812",
    "name": "PWWP domain profile",
    "representative": false,
    "score": null,
    "source": "profile",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 270
  },
  {
    "end": 349,
    "identifier": "PF00855",
    "integrated_identifier": "IPR000313",
    "model": "PF00855",
    "name": "PWWP domain",
    "representative": false,
    "score": 7.1e-15,
    "source": "pfam",
    "source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q9BZ95/?page_size=200",
    "start": 271
  }
]

PWWP1 · source-classified Phase 6A evidence

Ligands & Bioactivity

Explore all domain compounds →

19 chemical or preparation profiles · 13 domain-attributed assay / association observations. Counts refer to the curated snapshot.

9 profiles

Deposited research ligands

BI-93213 observations · 1 research-ligand entries2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid0 observations · 1 research-ligand entries3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)-1,2-oxazole0 observations · 1 research-ligand entries3,5-dimethyl-4-(4-pyridin-4-yl-1~{H}-pyrazol-3-yl)-1,2-oxazole0 observations · 1 research-ligand entries4-(3-methyl-5-phenyl-imidazol-4-yl)pyridine0 observations · 1 research-ligand entries4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-1,2-oxazole0 observations · 1 research-ligand entries5-methyl-2-piperidin-4-yl-6-pyridin-4-yl-pyridazin-3-one0 observations · 1 research-ligand entries5-methyl-6-phenyl-2-piperidin-4-yl-pyridazin-3-one0 observations · 1 research-ligand entries[3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)phenyl]methanamine0 observations · 1 research-ligand entries

8 profiles

Studied without research structure

compound 11 (Collie 2025)1 observations · 0 research-ligand entriescompound 12 (Collie 2025)1 observations · 0 research-ligand entriescompound 13 (Collie 2025)1 observations · 0 research-ligand entriescompound 5 (Collie 2025)1 observations · 0 research-ligand entriescompound 6 (Collie 2025)1 observations · 0 research-ligand entriescompound 7 (Collie 2025)1 observations · 0 research-ligand entriesMS97151 observations · 0 research-ligand entriesUNC69341 observations · 0 research-ligand entries

0 profiles

Ambiguous / indirect evidence

No records in this category for the selected domain in the curated snapshot.

1 other deposited components in this domain (not pharmacological ligands)

Buffers, ions, cryoprotectants and solvents remain recorded as deposited chemical components.

4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID · Other PDB component · not a studied ligand
3 protein-level observations — no specific PWWP-domain attribution

These observations concern NSD3 in its reported experimental context. They are excluded from the selected domain's measurement counts.

Open this domain in Structural & Binding Landscape →

Phase 6B · newly investigated source evidence

Additional experimental observations

Explore Phase 6B evidence

No newly accepted exact-domain observations for this specific PWWP instance.

9 source-reported NSD3 PWWP results with an unresolved domain instance

PWWP1/PWWP2 attribution and the actual purified construct are not verified. These are excluded from exact-domain counts.

No new unmodified parent binary PWWP-bound PDB structure is claimed for these entries. Original Phase 5/6A numbers remain unchanged.

PWWP1 · Deposited coordinates

Experimental coverage and AlphaFold correspondence

11 entry / domain records

One representative chain per PDB entry and native domain. RMSD uses fixed UniProt correspondence and all common Cα atoms; it is reported only for ≥40 atoms and ≥80% core coverage. A value is descriptive, not a prediction benchmark.

PDBChainObserved core CαClassMethod / resolutionAF RMSD ÅReview
6G24A64 / 64Co-CrystalsX-RAY DIFFRACTION
2.1 Å		0.679No classification flag
6G25A64 / 64Co-CrystalsX-RAY DIFFRACTION
1.432 Å		0.512No classification flag
6G27A64 / 64Co-CrystalsX-RAY DIFFRACTION
1.65 Å		0.389No classification flag
6G29A64 / 64Co-CrystalsX-RAY DIFFRACTION
1.7 Å		0.423No classification flag
6G2BA64 / 64Co-CrystalsX-RAY DIFFRACTION
1.61 Å		0.444No classification flag
6G2CA64 / 64Co-CrystalsX-RAY DIFFRACTION
1.76 Å		0.461No classification flag
6G2EA64 / 64Co-CrystalsX-RAY DIFFRACTION
1.85 Å		0.465No classification flag
6G2FA64 / 64Co-CrystalsX-RAY DIFFRACTION
1.74 Å		0.455No classification flag
6G2OA64 / 64Co-CrystalsX-RAY DIFFRACTION
1.81 Å		0.474No classification flag
6G3PA64 / 64APOX-RAY DIFFRACTION
2.8 Å		0.701No classification flag
6G3TA64 / 64APOX-RAY DIFFRACTION
2.53 Å		0.663No classification flag

PWWP1 · Measured preparations

Frozen v1.2 assay records

Explore evidence links

This retained table is the original source projection. The Phase 5 Ligands & Bioactivity section above includes added observations and reviewed target context. Values remain attached to their assay, construct and preparation. A crystal structure does not transfer affinity to another construct or stereoisomer. Assay pages preserve field-level source-verification states where reviewed; unreviewed null fields remain uncurated.

Preparation / identityAssay and resultConstructEvidence and source
BI-9321
exact single CCD identity		SPR Kd
= 166.0 nM ± 3.0
direct binding affinity		263–398PMID:31285596
Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page

Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. Exact assay temperature, mutations and per-dose contact times remain not inspected.

Assay conditions and interpretation

{}

Primary developer website; original full article assay table was not retrieved.

BI-9321
exact single CCD identity		NanoBRET IC50
= 1.2 µM ± 0.06
cellular interaction response		UncuratedPMID:31285596
Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page

The value 1.2 ± 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.

Assay conditions and interpretation

{"cell_line": "U2OS"}

Interpretation not recorded in this snapshot.

UNC6934
exact single CCD identity		SPR Kd counter-screen
> 30.0 µM
censored binding limit		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 11 (Collie 2025)
assayed stereoisomeric mixture not single chemical identity		SPR Kd counter-screen
No binding
negative binding test		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 12 (Collie 2025)
paper label exact identity unresolved		SPR Kd counter-screen
No binding
negative binding test		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 13 (Collie 2025)
paper label exact identity unresolved		SPR Kd counter-screen
No binding
negative binding test		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 5 (Collie 2025)
assayed stereoisomeric mixture not single chemical identity		SPR Kd counter-screen
> 30.0 µM
censored binding limit		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 6 (Collie 2025)
paper label exact identity unresolved		SPR Kd counter-screen
> 30.0 µM
censored binding limit		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

compound 7 (Collie 2025)
exact single CCD identity		SPR Kd counter-screen
> 30.0 µM
censored binding limit		263–398PMID:40959233
Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected

Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.

Assay conditions and interpretation

{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}

Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.

Scientific review queue

PWWP1 · Prediction evidence

Predicted models

5 model records

Domain retention uses independently reconstructed UniProt isoform edits. Local pLDDT is not experimental confirmation and does not establish interdomain orientation.

ModelOriginCore retentionCore mean pLDDTFull mean pLDDTCautions
AF-Q9BZ95-F1:v6
Canonical		GDMcomplete89.461.9
AF-Q9BZ95-2-F1:v6GDMcomplete9063.8
AF-Q9BZ95-3-F1:v6GDMcomplete93.954.6
AF-Q9BZ95-4-F1:v6GDMcomplete89.763.6
AF-Q9BZ95-5-F1:v6GDMcomplete89.461.5

PWWP1 · Structural correspondence

Human annotation-core comparisons

17 pairs

Structural alignment establishes a residue correspondence for these cropped cores. It does not establish equivalent ligand pockets, function or selectivity.

Domain pairAligned CαUS-align RMSD ÅTM score A / BView
ARID4A PWWP1 NSD3 PWWP1562.170.5 / 0.68Aligned core viewer
BRD1 PWWP1 NSD3 PWWP1572.210.563 / 0.707Aligned core viewer
BRPF1 PWWP1 NSD3 PWWP1592.120.595 / 0.752Aligned core viewer
BRPF3 PWWP1 NSD3 PWWP1592.060.593 / 0.746Aligned core viewer
DNMT3A PWWP1 NSD3 PWWP1561.70.794 / 0.74Aligned core viewer
DNMT3B PWWP1 NSD3 PWWP1561.680.784 / 0.732Aligned core viewer
HDGF PWWP1 NSD3 PWWP1532.440.653 / 0.608Aligned core viewer
HDGFL2 PWWP1 NSD3 PWWP1561.960.791 / 0.727Aligned core viewer
HDGFL3 PWWP1 NSD3 PWWP1561.960.774 / 0.713Aligned core viewer
MSH6 PWWP1 NSD3 PWWP1631.620.839 / 0.828Aligned core viewer
NSD2 PWWP1 NSD3 PWWP1630.980.922 / 0.936Aligned core viewer
NSD3 PWWP1 NSD3 PWWP2552.40.661 / 0.669Aligned core viewer
NSD3 PWWP1 PSIP1 PWWP1562.530.654 / 0.654Aligned core viewer
NSD3 PWWP1 PWWP2B PWWP1562.090.741 / 0.773Aligned core viewer
NSD3 PWWP1 PWWP3A PWWP1532.170.627 / 0.643Aligned core viewer
NSD3 PWWP1 ZMYND11 PWWP1521.850.697 / 0.833Aligned core viewer
NSD3 PWWP1 ZMYND8 PWWP1511.440.693 / 0.839Aligned core viewer