Ligand profile

PY5

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

Bound to: KP13_04181 — Aspartate aminotransferase

Via homolog PDB 1cq7 UniProt P00509 Formula C₁₃H₂₁N₂O₇P
Mol. weight 348.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PY5
PDB
1cq7
UniProt (similar protein)
P00509
Target protein
KP13_04181

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 348.29 Da
LogP (Crippen) 1.05
H-bond donors 5
H-bond acceptors 6
TPSA 149.21 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.54
Formula C₁₃H₂₁N₂O₇P

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 149.2
  • −1 ≤ LogP ≤ 5 1.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 348.3
  • LogP ≤ 5 1.05
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 149.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
InChI 
InChI=1S/C13H21N2O7P/c1-3-4-11(13(17)18)15-6-10-9(7-22-23(19,20)21)5-14-8(2)12(10)16/h5,11,15-16H,3-4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/t11-/m0/s1
InChIKey 
YYAMSLLSQINIQO-NSHDSACASA-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
PF00155

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_04181.

PDB 38

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

Ligand PDB entry

ChEMBL 1

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)