Ligand profile

GT0

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

Bound to: KP13_05165 — Pyridoxamine kinase

Via homolog PDB 4en4 UniProt O00764 Formula C₉H₁₃NO₃
Mol. weight 183.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GT0
PDB
4en4
UniProt (similar protein)
O00764
Target protein
KP13_05165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 183.21 Da
LogP (Crippen) 0.73
H-bond donors 2
H-bond acceptors 4
TPSA 62.58 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.44
Formula C₉H₁₃NO₃

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 62.6
  • −1 ≤ LogP ≤ 5 0.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 183.2
  • LogP ≤ 5 0.73
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 62.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)CO)COC)O
InChI 
InChI=1S/C9H13NO3/c1-6-9(12)8(5-13-2)7(4-11)3-10-6/h3,11-12H,4-5H2,1-2H3
InChIKey 
SVINQHQHARVZFF-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
PF08543

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_05165.

PDB 12

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

Ligand PDB entry

ChEMBL 5

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)