Ligand profile

CHEMBL3235084

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₁H₂₃N₅O₃S
pchembl 7.52 ~30.2 nM
Mol. weight 425.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3235084
UniProt (similar protein)
P0A0K8
pchembl
7.520 (~30.2 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.51 Da
LogP (Crippen) 4.40
H-bond donors 3
H-bond acceptors 6
TPSA 117.10 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.29
Formula C₂₁H₂₃N₅O₃S

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 117.1
  • −1 ≤ LogP ≤ 5 4.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 425.5
  • LogP ≤ 5 4.40
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 117.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(-c2nc(C(C)(C)C)cs2)c(-c2cncc(C(=O)O)c2)cn1
InChI 
InChI=1S/C21H23N5O3S/c1-5-23-20(29)26-17-7-14(18-25-16(11-30-18)21(2,3)4)15(10-24-17)12-6-13(19(27)28)9-22-8-12/h6-11H,5H2,1-4H3,(H,27,28)(H2,23,24,26,29)
InChIKey 
OMJBZCVTMXZQCE-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)