Binder profile

KDH

Bioactivity hit from ChEMBL on a similar protein.

Bound to: PA4089 — 3-ketoacyl-ACP reductase

Via homolog UniProt Q8I2S7 C22H18O11
pchembl 6.50
Mol. weight 458.38 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
KDH
UniProt (similar protein)
Q8I2S7
pchembl
6.500
Target protein
PA4089

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 458.38 Da
LogP (Crippen) 2.23
H-bond donors 8
H-bond acceptors 11
TPSA 197.37 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.14
Formula C22H18O11

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.

Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 458.4
  • LogP ≤ 5 2.23
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 197.4
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 
c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)O)OC(=O)c4cc(c(c(c4)O)O)O
InChI 
InChI=1S/C22H18O11/c23-10-5-12(24)11-7-18(33-22(31)9-3-15(27)20(30)16(28)4-9)21(32-17(11)6-10)8-1-13(25)19(29)14(26)2-8/h1-6,18,21,23-30H,7H2/t18-,21-/m1/s1
InChIKey 
WMBWREPUVVBILR-WIYYLYMNSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF00106

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4089.

PDB 3

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

Ligand PDB entry

ChEMBL 4

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)