Ligand profile

087

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 3u2k UniProt P0A0K8 Formula C₁₇H₁₈Cl₃N₅O₂
Mol. weight 430.72 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
087
PDB
3u2k
UniProt (similar protein)
P0A0K8
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 430.72 Da
LogP (Crippen) 3.18
H-bond donors 3
H-bond acceptors 4
TPSA 104.11 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.35
Formula C₁₇H₁₈Cl₃N₅O₂

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 104.1
  • −1 ≤ LogP ≤ 5 3.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 430.7
  • LogP ≤ 5 3.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 104.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c([nH]1)C(=O)NC2CCN(CC2)c3cc(cc(n3)Cl)C(=O)N)Cl)Cl
InChI 
InChI=1S/C17H18Cl3N5O2/c1-8-13(19)14(20)15(22-8)17(27)23-10-2-4-25(5-3-10)12-7-9(16(21)26)6-11(18)24-12/h6-7,10,22H,2-5H2,1H3,(H2,21,26)(H,23,27)
InChIKey 
DDZQOAWVENUEIU-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
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 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)