Ligand profile

HFC

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 7dqi UniProt P0AES6 Formula C₉H₆O₄
Mol. weight 178.14 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
HFC
PDB
7dqi
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 178.14 Da
LogP (Crippen) 1.20
H-bond donors 2
H-bond acceptors 4
TPSA 70.67 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 13
Fraction sp³ C 0.00
Formula C₉H₆O₄

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 70.7
  • −1 ≤ LogP ≤ 5 1.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 178.1
  • LogP ≤ 5 1.20
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 70.7
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(cc(c1O)O)OC(=O)C=C2
InChI 
InChI=1S/C9H6O4/c10-6-3-5-1-2-9(12)13-8(5)4-7(6)11/h1-4,10-11H
InChIKey 
ILEDWLMCKZNDJK-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF02518

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_00051.

PDB 87

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)