Ligand profile

CHEMBL3809316

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₁₆H₁₃N₅OS
pchembl 7.70 ~20.0 nM
Mol. weight 323.38 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3809316
UniProt (similar protein)
P0A0K8
pchembl
7.700 (~20.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.38 Da
LogP (Crippen) 2.93
H-bond donors 1
H-bond acceptors 6
TPSA 76.46 Ų
Rotatable bonds 3
Aromatic rings 4 / 4
Heavy atoms 23
Fraction sp³ C 0.12
Formula C₁₆H₁₃N₅OS

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 76.5
  • −1 ≤ LogP ≤ 5 2.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.4
  • LogP ≤ 5 2.93
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 76.5
PAINS Alert

Matches PAINS filter: dyes5A(27). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCn1c(=O)ccc2c(-c3cnc(-c4cccnc4)s3)n[nH]c21
InChI 
InChI=1S/C16H13N5OS/c1-2-21-13(22)6-5-11-14(19-20-15(11)21)12-9-18-16(23-12)10-4-3-7-17-8-10/h3-9H,2H2,1H3,(H,19,20)
InChIKey 
BGLANQCMTSXFSJ-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)