Ligand profile

CHEMBL3739786

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₁₉H₁₉N₄O₄PS
pchembl 8.05 ~8.9 nM
Mol. weight 430.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3739786
UniProt (similar protein)
P0A0K8
pchembl
8.050 (~8.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 430.43 Da
LogP (Crippen) 4.31
H-bond donors 3
H-bond acceptors 6
TPSA 121.22 Ų
Rotatable bonds 7
Aromatic rings 4 / 4
Heavy atoms 29
Fraction sp³ C 0.21
Formula C₁₉H₁₉N₄O₄PS

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 121.2
  • −1 ≤ LogP ≤ 5 4.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 430.4
  • LogP ≤ 5 4.31
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 121.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCc1cccc2c(-c3cnc(-c4ccc(COP(=O)(O)O)nc4)s3)n[nH]c12
InChI 
InChI=1S/C19H19N4O4PS/c1-2-4-12-5-3-6-15-17(12)22-23-18(15)16-10-21-19(29-16)13-7-8-14(20-9-13)11-27-28(24,25)26/h3,5-10H,2,4,11H2,1H3,(H,22,23)(H2,24,25,26)
InChIKey 
GXXVPQHRHZISDI-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)