Ligand profile

1A0

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 4hxw UniProt Q839Z1 Formula C₁₉H₁₉ClN₈S
Mol. weight 426.94 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1A0
PDB
4hxw
UniProt (similar protein)
Q839Z1
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.94 Da
LogP (Crippen) 3.20
H-bond donors 2
H-bond acceptors 8
TPSA 109.50 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 29
Fraction sp³ C 0.32
Formula C₁₉H₁₉ClN₈S

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 109.5
  • −1 ≤ LogP ≤ 5 3.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.9
  • LogP ≤ 5 3.20
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 109.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nccn5)nc4)Cl
InChI 
InChI=1S/C19H19ClN8S/c1-2-12-15(20)14-17(25-12)26-19(27-18(14)28-6-3-10(21)9-28)29-11-7-13-16(24-8-11)23-5-4-22-13/h4-5,7-8,10H,2-3,6,9,21H2,1H3,(H,25,26,27)/t10-/m1/s1
InChIKey 
WXCUMDKJRMUULE-SNVBAGLBSA-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)