Ligand profile

CHEMBL3235078

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₁₆H₁₅N₅O₂S
pchembl 7.41 ~38.9 nM
Mol. weight 341.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3235078
UniProt (similar protein)
P0A0K8
pchembl
7.410 (~38.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 341.40 Da
LogP (Crippen) 2.60
H-bond donors 3
H-bond acceptors 5
TPSA 110.00 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.12
Formula C₁₆H₁₅N₅O₂S

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 110.0
  • −1 ≤ LogP ≤ 5 2.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 341.4
  • LogP ≤ 5 2.60
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 110.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1ccc(-c2nc3cccc(C(N)=O)c3s2)cn1
InChI 
InChI=1S/C16H15N5O2S/c1-2-18-16(23)21-12-7-6-9(8-19-12)15-20-11-5-3-4-10(14(17)22)13(11)24-15/h3-8H,2H2,1H3,(H2,17,22)(H2,18,19,21,23)
InChIKey 
HRMROSXWRLSVKN-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)