Ligand profile

1A1

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 4hyp UniProt P0AES6 Formula C₁₇H₁₃N₇OS
Mol. weight 363.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1A1
PDB
4hyp
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 363.41 Da
LogP (Crippen) 2.68
H-bond donors 1
H-bond acceptors 8
TPSA 98.48 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 26
Fraction sp³ C 0.18
Formula C₁₇H₁₃N₇OS

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 98.5
  • −1 ≤ LogP ≤ 5 2.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 363.4
  • LogP ≤ 5 2.68
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cnc1)c2nc3c(nc(nc3s2)NC(=O)C4CC4)n5ccnc5
InChI 
InChI=1S/C17H13N7OS/c25-14(10-3-4-10)22-17-21-13(24-7-6-19-9-24)12-16(23-17)26-15(20-12)11-2-1-5-18-8-11/h1-2,5-10H,3-4H2,(H,21,22,23,25)
InChIKey 
GEKYZKWDAFEGJJ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)