Ligand profile

Q52

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6z1a UniProt P0A0K8 Formula C₂₃H₂₇ClN₄O
Mol. weight 410.95 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Q52
PDB
6z1a
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 410.95 Da
LogP (Crippen) 4.09
H-bond donors 1
H-bond acceptors 5
TPSA 50.28 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.39
Formula C₂₃H₂₇ClN₄O

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 50.3
  • −1 ≤ LogP ≤ 5 4.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 410.9
  • LogP ≤ 5 4.09
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 50.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(n1)c(ccn2)CCN3CCC(CC3)NCc4ccc(cc4)Cl
InChI 
InChI=1S/C23H27ClN4O/c1-29-22-7-6-21-23(27-22)18(8-12-25-21)9-13-28-14-10-20(11-15-28)26-16-17-2-4-19(24)5-3-17/h2-8,12,20,26H,9-11,13-16H2,1H3
InChIKey 
MLGPJPYFHAIWJL-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
PDB
Binding sites
PF00521

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 87

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

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)