Ligand profile

HPV

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02169 — D-3-phosphoglycerate dehydrogenase

Via homolog PDB 3ddn UniProt P9WNX3 Formula C₃H₅O₇P
Mol. weight 184.04 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HPV
PDB
3ddn
UniProt (similar protein)
P9WNX3
Target protein
KP13_02169

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 184.04 Da
LogP (Crippen) -1.25
H-bond donors 3
H-bond acceptors 4
TPSA 121.13 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.33
Formula C₃H₅O₇P

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 121.1
  • −1 ≤ LogP ≤ 5 -1.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 184.0
  • LogP ≤ 5 -1.25
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 121.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)C(=O)O)OP(=O)(O)O
InChI 
InChI=1S/C3H5O7P/c4-2(3(5)6)1-10-11(7,8)9/h1H2,(H,5,6)(H2,7,8,9)
InChIKey 
LFLUCDOSQPJJBE-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00389' 'PF02826

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02169.

PDB 19

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)