Ligand profile

CHEMBL3741475

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₀H₁₈N₄O₂S
pchembl 7.92 ~12.0 nM
Mol. weight 378.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3741475
UniProt (similar protein)
P0A0K8
pchembl
7.920 (~12.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.46 Da
LogP (Crippen) 4.71
H-bond donors 2
H-bond acceptors 5
TPSA 91.76 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 27
Fraction sp³ C 0.20
Formula C₂₀H₁₈N₄O₂S

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.

  • TPSA ≤ 90 Ų 91.8
  • −1 ≤ LogP ≤ 5 4.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.5
  • LogP ≤ 5 4.71
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 91.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCc1cccc2c(-c3cnc(-c4cnc(C(=O)O)cc4C)s3)n[nH]c12
InChI 
InChI=1S/C20H18N4O2S/c1-3-5-12-6-4-7-13-17(12)23-24-18(13)16-10-22-19(27-16)14-9-21-15(20(25)26)8-11(14)2/h4,6-10H,3,5H2,1-2H3,(H,23,24)(H,25,26)
InChIKey 
YNICTVRWIBIRBP-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.

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)