Ligand profile

PPJ

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

Bound to: KP13_02775 — Cystathionine beta-lyase metC

Via homolog PDB 1e5e UniProt A2FEV4 Formula C₁₃H₁₉N₂O₈P
Mol. weight 362.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPJ
PDB
1e5e
UniProt (similar protein)
A2FEV4
Target protein
KP13_02775

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 362.28 Da
LogP (Crippen) 0.35
H-bond donors 5
H-bond acceptors 7
TPSA 169.77 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.46
Formula C₁₃H₁₉N₂O₈P

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 169.8
  • −1 ≤ LogP ≤ 5 0.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 362.3
  • LogP ≤ 5 0.35
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 169.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H](C[C@H](C)O)C(=O)O)O
InChI 
InChI=1S/C13H19N2O8P/c1-7(16)3-11(13(18)19)15-5-10-9(6-23-24(20,21)22)4-14-8(2)12(10)17/h4-5,7,11,16-17H,3,6H2,1-2H3,(H,18,19)(H2,20,21,22)/b15-5+/t7-,11-/m0/s1
InChIKey 
XZPXXYMXESJHME-PMICCBOBSA-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
PF01053

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_02775.

PDB 16

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

Ligand PDB entry

ChEMBL 4

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)