Ligand profile

HE9

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 7dpr UniProt P0AES6 Formula C₈H₈O₄
Mol. weight 168.15 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
HE9
PDB
7dpr
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 168.15 Da
LogP (Crippen) 0.88
H-bond donors 2
H-bond acceptors 4
TPSA 66.76 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.12
Formula C₈H₈O₄

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 66.8
  • −1 ≤ LogP ≤ 5 0.88
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 168.1
  • LogP ≤ 5 0.88
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 66.8
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 
COC(=O)c1ccc(c(c1)O)O
InChI 
InChI=1S/C8H8O4/c1-12-8(11)5-2-3-6(9)7(10)4-5/h2-4,9-10H,1H3
InChIKey 
CUFLZUDASVUNOE-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)