Ligand profile

CHEMBL3810056

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₄H₂₇N₇O₃S
pchembl 7.89 ~12.9 nM
Mol. weight 493.59 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3810056
UniProt (similar protein)
P0A0K8
pchembl
7.890 (~12.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 493.59 Da
LogP (Crippen) 2.38
H-bond donors 2
H-bond acceptors 9
TPSA 118.03 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 35
Fraction sp³ C 0.38
Formula C₂₄H₂₇N₇O₃S

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 118.0
  • −1 ≤ LogP ≤ 5 2.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 493.6
  • LogP ≤ 5 2.38
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 118.0
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 
CCCn1c(=O)ccc2c(-c3cnc(-c4ccc(C(=O)NCCN5CCOCC5)nc4)s3)n[nH]c21
InChI 
InChI=1S/C24H27N7O3S/c1-2-8-31-20(32)6-4-17-21(28-29-22(17)31)19-15-27-24(35-19)16-3-5-18(26-14-16)23(33)25-7-9-30-10-12-34-13-11-30/h3-6,14-15H,2,7-13H2,1H3,(H,25,33)(H,28,29)
InChIKey 
JRFZLLFSYNBRHC-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)