Ligand profile

HPK

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

Bound to: KP13_04610 — 2-hydroxy-6-oxononadienedioate/2-hydroxy-6- oxononatrienedioate hydrolase

Via homolog PDB 2wug UniProt P9WNH5 Formula C₁₂H₉O₄⁻
Mol. weight 217.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HPK
PDB
2wug
UniProt (similar protein)
P9WNH5
Target protein
KP13_04610

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 217.20 Da
LogP (Crippen) 0.13
H-bond donors 0
H-bond acceptors 4
TPSA 74.27 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.08
Formula C₁₂H₉O₄⁻

Drug-likeness

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

Permeability proxy High

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 74.3
  • −1 ≤ LogP ≤ 5 0.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 217.2
  • LogP ≤ 5 0.13
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 74.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C(=O)C\C=C\C(=O)C(=O)[O-]
InChI 
InChI=1S/C12H10O4/c13-10(9-5-2-1-3-6-9)7-4-8-11(14)12(15)16/h1-6,8H,7H2,(H,15,16)/p-1/b8-4+
InChIKey 
QPGAZPBFRAAJBD-XBXARRHUSA-M

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
PF00561

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_04610.

PDB 22

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)