Ligand profile

PDG

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

Bound to: KP13_04181 — Aspartate aminotransferase

Via homolog PDB 1x2a UniProt P00509 Formula C₁₃H₁₉N₂O₉P
Mol. weight 378.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PDG
PDB
1x2a
UniProt (similar protein)
P00509
Target protein
KP13_04181

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.27 Da
LogP (Crippen) 0.11
H-bond donors 6
H-bond acceptors 7
TPSA 186.51 Ų
Rotatable bonds 10
Aromatic rings 1 / 1
Heavy atoms 25
Fraction sp³ C 0.46
Formula C₁₃H₁₉N₂O₉P

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 186.5
  • −1 ≤ LogP ≤ 5 0.11
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 378.3
  • LogP ≤ 5 0.11
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 186.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCC(=O)O)C(=O)O)O
InChI 
InChI=1S/C13H19N2O9P/c1-7-12(18)9(8(4-14-7)6-24-25(21,22)23)5-15-10(13(19)20)2-3-11(16)17/h4,10,15,18H,2-3,5-6H2,1H3,(H,16,17)(H,19,20)(H2,21,22,23)/t10-/m1/s1
InChIKey 
JMRKOGDJNHPMHS-SNVBAGLBSA-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)