Resolved chemical identity

(4S)-2-METHYL-2,4-PENTANEDIOL

Other PDB component · not a studied ligand

complete_deposited_InChIKey

0 assay / association records0 preparations0 research-ligand PDB entries

No deposited PWWP research-ligand geometry is classified for this preparation in the selected release. Deposition of a buffer/ion is not binding evidence.

Clinical / development status: Not independently curated. A chemical probe classification does not imply medicinal approval.

Identity is separate from preparation

Chemical identity

Stable identity: INCHIKEY:SVTBMSDMJJWYQN-YFKPBYRVSA-N
Full InChIKey: SVTBMSDMJJWYQN-YFKPBYRVSA-N
Source identity status: complete deposited InChIKey
Deposited CCD identifiers: MPD
External identifiers: See deposited identity and source links

Reference formula: C6H14O2
Calculated molecular weight: 118.176
Calculated descriptors: cLogP 0.5282 · TPSA 40.46 Å² · HBD 2 · HBA 2RDKit 2025.09.3; calculations for this source identity, not experimental measurements.
Depiction validation: verified smiles full inchikey match

SMILES, InChI & complete identity record

Isomeric SMILES: C[C@@H](CC(C)(C)O)O
InChI: Not curated

{
  "aliases": [
    "(4S)-2-METHYL-2,4-PENTANEDIOL"
  ],
  "ccd_ids": [
    "MPD"
  ],
  "ccd_names": "[\"(4S)-2-METHYL-2,4-PENTANEDIOL\"]",
  "ccd_types": "[\"non-polymer\"]",
  "chemical_id": "INCHIKEY:SVTBMSDMJJWYQN-YFKPBYRVSA-N",
  "connectivity_block": "SVTBMSDMJJWYQN",
  "curated_source_sha256": null,
  "curation_version": "frozen-v1.2",
  "external_identifiers": {},
  "formal_charge_by_ccd": "{\"MPD\": 0}",
  "formulae": "[\"C6 H14 O2\"]",
  "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.",
  "identity_status": "complete_deposited_InChIKey",
  "inchikey": "SVTBMSDMJJWYQN-YFKPBYRVSA-N",
  "inventory_origin": "v1_CCD_inventory",
  "isomeric_smiles": "C[C@@H](CC(C)(C)O)O",
  "primary_name": "(4S)-2-METHYL-2,4-PENTANEDIOL",
  "retrieval_date": "2026-10-24",
  "smiles_stereo_by_ccd": "{\"MPD\": \"C[C@@H](CC(C)(C)O)O\"}",
  "source_metadata_sha256": "{\"MPD\": \"36832cae97f8e82cc5e77ec4015974f0e5e89e2800696488c197e164c0ddac80\"}",
  "source_urls": [
    "https://www.rcsb.org/ligand/MPD"
  ]
}

Measured target and original context

Bioactivity & experimental observations

Download assay CSV

Each row is one source-specific observation. Repeated measurements of this compound are not independent compounds. Direct binding, functional displacement and cellular outcomes retain their distinct endpoints.

Preparation	Tested target & construct	Method / endpoint	Original observation	Conditions & uncertainty	Source & verification
No observations match these filters. Missing curation is not evidence of biological inactivity.

Exact deposited instances

Experimental structures

Native-core and broader Pfam proximity are distinguished from contacts elsewhere in a protein. Each action opens the actual deposited ligand instance. Geometric proximity does not supply a measured binding affinity.

Entry / ligand	Native domain & protein chain	Geometric evidence	Minimum distance	Inspect
5XSK · MPDPDB:5XSK:LIG:E:MPD:201:.	Hdgf PWWP1Protein label chain C · ligand label chain E	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 3.271 Å Pfam: 3.271 Å	View deposited instance
5XSK · MPDPDB:5XSK:LIG:E:MPD:201:.	Hdgf PWWP1Protein label chain D · ligand label chain E	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 3.3838 Å Pfam: 3.3838 Å	View deposited instance
5XSK · MPDPDB:5XSK:LIG:F:MPD:201:.	Hdgf PWWP1Protein label chain C · ligand label chain F	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 3.4287 Å Pfam: 3.4287 Å	View deposited instance
5XSK · MPDPDB:5XSK:LIG:F:MPD:201:.	Hdgf PWWP1Protein label chain D · ligand label chain F	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 3.154 Å Pfam: 3.154 Å	View deposited instance
9I7H · MPDPDB:9I7H:LIG:C:MPD:101:.	HDGFL2 PWWP1Protein label chain A · ligand label chain C	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 2.9604 Å Pfam: 2.9604 Å	View deposited instance
9I7H · MPDPDB:9I7H:LIG:D:MPD:101:.	HDGFL2 PWWP1Protein label chain B · ligand label chain D	native annotation core contactcrystallization additivecrystallization additive · other component. Deposited geometry is not solution affinity.	Core: 2.8356 Å Pfam: 2.8356 Å	View deposited instance

Preparations, identities and controls remain separate

Experimental context

No measured preparation is linked to this deposited identity in the curated snapshot.

Provenance and reproducibility

Sources & downloads

https://www.rcsb.org/ligand/MPD

Download complete evidence JSON Curation methods & source receipts

Snapshot 2026-10-26 · phase5-1.0.0 · original measurements, operators, constructs and uncertainty are retained in the exports.