Experimental coordinates · Exact deposited instances
Ligand contacts & pocket quality
Inspect the atoms that are present, the residues that are missing, and the precise scope of each chemical association.
Phase 6C historical atom / receptor assessment Phase 6C.1 full-atom experimental quality inventory
Full-coordinate Phase 6C.1 atom and ligand environment assessment
Load the checksum-verified original coordinates to explore the selected chain and ligand.
Drag to rotate · scroll to zoom · arrow keys rotate · + / − zoom · Home resets. Select a residue below to highlight its observed atoms.
Atom completeness · selected chain and annotation core
What can these coordinates support?
A fully observed annotation core is not a complete-receptor certification. Short annotation intervals, absent peripheral residues, alternate conformers and unexamined density can limit structural interpretation. No receptor preparation was performed.
Frozen 5 Å heavy-atom proximity observations
Contacting residues · Y6V
Heavy-atom distances use the first deposited model and asymmetric unit, occupancy >0 and retained alternate locations. No symmetry expansion or affinity inference. Proximity alone is not evidence of affinity or a functional interaction.
| Canonical residue | Deposited residue | Scope | Minimum distance | Atom quality | Inspect |
|---|---|---|---|---|---|
| VAL 230 | B:230 · entity 20 · label B | annotation core | 3.6431 Å | Unassessed | |
| TYR 233 | B:233 · entity 23 · label B | annotation core | 3.2485 Å | Unassessed | |
| PRO 234 | B:234 · entity 24 · label B | annotation core | 4.8800 Å | Unassessed | |
| TRP 236 | B:236 · entity 26 · label B | annotation core | 3.5708 Å | Unassessed | |
| PHE 266 | B:266 · entity 56 · label B | annotation core | 3.3453 Å | Unassessed | |
| PHE 267 | B:267 · entity 57 · label B | annotation core | 3.3191 Å | Unassessed | |
| GLY 268 | B:268 · entity 58 · label B | annotation core | 3.2011 Å | Unassessed | |
| ASP 269 | B:269 · entity 59 · label B | annotation core | 3.3369 Å | Unassessed | |
| ALA 270 | B:270 · entity 60 · label B | annotation core | 2.9349 Å | Unassessed | |
| PRO 271 | B:271 · entity 61 · label B | annotation core | 4.1778 Å | Unassessed | |
| GLU 272 | B:272 · entity 62 · label B | annotation core | 3.4783 Å | Unassessed | |
| ARG 273 | B:273 · entity 63 · label B | annotation core | 3.5568 Å | Unassessed | |
| ALA 274 | B:274 · entity 64 · label B | annotation core | 3.7369 Å | Unassessed | |
| LEU 318 | B:318 · entity 108 · label B | broader Pfam PWWP | 3.8129 Å | Unassessed | |
| GLN 321 | B:321 · entity 111 · label B | broader Pfam PWWP | 2.9375 Å | Unassessed |
Identity, native target and exact site links
Linked experimental assays
| Measured preparation | Method / endpoint | Original observation | Tested construct | Evidence |
|---|---|---|---|---|
| MRT866 | SPR Kd · | = 349.0 nM | Unknown–Unknown | PWWP:ASSAY:0003 same exact chemical identity and native domain; construct equivalence not assumed |
Filterable structural assessment inventory
Coordinate coverage & quality
| PDB / chain | Domain | Core Cα coverage | PWWP-contact ligand instances | Atom assessment | Missing core heavy atoms |
|---|---|---|---|---|---|
| 29HG · B | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
| 29HH · B | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
| 29HI · B | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
| 5VC8 · A | NSD2 PWWP1 | 60 / 65 | 23 | Unassessed | — |
| 5VC8 · B | NSD2 PWWP1 | 65 / 65 | 17 | Unassessed | — |
| 6UE6 · A | NSD2 PWWP1 | 62 / 65 | 11 | Unassessed | — |
| 6UE6 · B | NSD2 PWWP1 | 65 / 65 | 14 | Unassessed | — |
| 6UE6 · C | NSD2 PWWP1 | 62 / 65 | 12 | Unassessed | — |
| 6UE6 · D | NSD2 PWWP1 | 61 / 65 | 7 | Unassessed | — |
| 6UE6 · E | NSD2 PWWP1 | 63 / 65 | 7 | Unassessed | — |
| 6UE6 · F | NSD2 PWWP1 | 60 / 65 | 7 | Unassessed | — |
| 6UE6 · G | NSD2 PWWP1 | 62 / 65 | 14 | Unassessed | — |
| 6UE6 · H | NSD2 PWWP1 | 60 / 65 | 9 | Unassessed | — |
| 6XCG · A | NSD2 PWWP1 | 65 / 65 | 1 | Assessed | 6 |
| 6XCG · B | NSD2 PWWP1 | 65 / 65 | 4 | Assessed | 12 |
| 6XCG · C | NSD2 PWWP1 | 63 / 65 | 5 | Assessed | 4 |
| 7LMT · A | NSD2 PWWP1 | 61 / 65 | 3 | Unassessed | — |
| 7LMT · B | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7LMT · C | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7LMT · D | NSD2 PWWP1 | 62 / 65 | 3 | Unassessed | — |
| 7LMT · E | NSD2 PWWP1 | 62 / 65 | 3 | Unassessed | — |
| 7LMT · F | NSD2 PWWP1 | 61 / 65 | 3 | Unassessed | — |
| 7LMT · G | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7LMT · H | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7MDN · A | NSD2 PWWP1 | 61 / 65 | 3 | Unassessed | — |
| 7MDN · B | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7MDN · C | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7MDN · D | NSD2 PWWP1 | 62 / 65 | 3 | Unassessed | — |
| 7MDN · E | NSD2 PWWP1 | 62 / 65 | 3 | Unassessed | — |
| 7MDN · F | NSD2 PWWP1 | 61 / 65 | 3 | Unassessed | — |
| 7MDN · G | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7MDN · H | NSD2 PWWP1 | 61 / 65 | 2 | Unassessed | — |
| 7VLN · A | NSD2 PWWP1 | 60 / 65 | 1 | Unassessed | — |
| 7VLN · B | NSD2 PWWP1 | 60 / 65 | 1 | Unassessed | — |
| 7VLN · C | NSD2 PWWP1 | 62 / 65 | 0 | Unassessed | — |
| 9EXW · A | NSD2 PWWP1 | 65 / 65 | 3 | Unassessed | — |
| 9EXW · B | NSD2 PWWP1 | 61 / 65 | 4 | Unassessed | — |
| 9EXX · A | NSD2 PWWP1 | 65 / 65 | 6 | Unassessed | — |
| 9EXX · B | NSD2 PWWP1 | 61 / 65 | 8 | Unassessed | — |
| 9EXY · A | NSD2 PWWP1 | 59 / 65 | 1 | Unassessed | — |
| 9EXY · B | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
| 9FOC · A | NSD2 PWWP1 | 65 / 65 | 2 | Unassessed | — |
| 9FOC · B | NSD2 PWWP1 | 65 / 65 | 2 | Unassessed | — |
| 9FOE · A | NSD2 PWWP1 | 58 / 65 | 1 | Unassessed | — |
| 9KN9 · A | NSD2 PWWP1 | 62 / 65 | 4 | Unassessed | — |
| 9KN9 · B | NSD2 PWWP1 | 62 / 65 | 4 | Unassessed | — |
| 9KNA · A | NSD2 PWWP1 | 62 / 65 | 11 | Unassessed | — |
| 9KNA · B | NSD2 PWWP1 | 62 / 65 | 11 | Unassessed | — |
| 9KNB · A | NSD2 PWWP1 | 59 / 65 | 2 | Unassessed | — |
| 9Y60 · A | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
| 9Y61 · A | NSD2 PWWP1 | 65 / 65 | 1 | Unassessed | — |
Source bytes, methods and provenance
Detailed atom completeness only for the three packaged original-coordinate files; quality uses observed atom-name union across positive-occupancy alternate conformers, with per-alt differences retained. Missing entire residues are separate. Nonstandard amino-acid templates are unassessed. No density reinterpretation, receptor repair, docking or MD.
Coordinate SHA-256: 411eea421108aa7f0e46d8c191904297040016aeabc0f48ef43d4a7503888c2a
Source PDB: https://www.rcsb.org/structure/7MDN. Original coordinate file: mmCIF. Original annotation and contact calculations are retained unchanged; the additional completeness assessment is PWWP_POCKET_QUALITY_1.0.0.
Methods and reproducible builder are included under analysis/phase5_pockets and scripts/build_phase5_pockets.py in the downloadable release.