Ligand profile

PPE

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

Bound to: KP13_05467 — Diaminobutyrate--2-oxoglutarate aminotransferase

Via homolog PDB 1wkh UniProt Q5SHH5 Formula C₁₃H₂₀N₂O₉P⁺
Mol. weight 379.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPE
PDB
1wkh
UniProt (similar protein)
Q5SHH5
Target protein
KP13_05467

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 379.28 Da
LogP (Crippen) -0.47
H-bond donors 6
H-bond acceptors 6
TPSA 187.76 Ų
Rotatable bonds 10
Aromatic rings 1 / 1
Heavy atoms 25
Fraction sp³ C 0.46
Formula C₁₃H₂₀N₂O₉P⁺

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 187.8
  • −1 ≤ LogP ≤ 5 -0.47
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 379.3
  • LogP ≤ 5 -0.47
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 187.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(c[nH+]1)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)/p+1/t10-/m0/s1
InChIKey 
JMRKOGDJNHPMHS-JTQLQIEISA-O

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
PF00202

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_05467.

PDB 7

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

Ligand PDB entry

ZINC 35

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)