Ligand profile

CHEMBL3739840

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₁₉H₁₆N₄O₃S

pchembl 7.96 ~11.0 nM

Mol. weight 380.43 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL3739840
UniProt (similar protein): P0A0K8
pchembl: 7.960 (~11.0 nM)
Target protein: KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 380.43 Da

LogP (Crippen) 4.10

H-bond donors 3

H-bond acceptors 6

TPSA 111.99 Å²

Rotatable bonds 5

Aromatic rings 4 / 4

Heavy atoms 27

Fraction sp³ C 0.16

Formula C₁₉H₁₆N₄O₃S

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 112.0
−1 ≤ LogP ≤ 5 4.10

Lipinski's Rule of Five Pass 0 violations

MW ≤ 500 Da 380.4
LogP ≤ 5 4.10
H-bond donors ≤ 5 3
H-bond acceptors ≤ 10 6

Veber's rules Pass

Rotatable bonds ≤ 10 5
TPSA ≤ 140 Å² 112.0

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

CCCc1cccc2c(-c3cnc(-c4cnc(C(=O)O)c(O)c4)s3)n[nH]c12

InChI

InChI=1S/C19H16N4O3S/c1-2-4-10-5-3-6-12-15(10)22-23-16(12)14-9-21-18(27-14)11-7-13(24)17(19(25)26)20-8-11/h3,5-9,24H,2,4H2,1H3,(H,22,23)(H,25,26)

InChIKey

WJDBOBHNPJXMAD-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: ChEMBL
Curation: pdb_similarity_tanimoto
Binding sites: PF02518

External resources

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

ChEMBL ChEMBL compound CHEMBL3739840 →
UniProt UniProt P0A0K8 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL3739840”) →

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00051.

PDB 88

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

Ligand PDB entry

ChEMBL 99

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)