Ligand profile

PPG

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

Bound to: VK055_4046 — cystathionine beta-lyase

Via homolog PDB 1cl2 UniProt P06721 Formula C₁₄H₂₀N₃O₈P
Mol. weight 389.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPG
PDB
1cl2
UniProt (similar protein)
P06721
Target protein
VK055_4046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 389.30 Da
LogP (Crippen) 0.22
H-bond donors 5
H-bond acceptors 8
TPSA 184.79 Ų
Rotatable bonds 10
Aromatic rings 1 / 1
Heavy atoms 26
Fraction sp³ C 0.36
Formula C₁₄H₂₀N₃O₈P

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 184.8
  • −1 ≤ LogP ≤ 5 0.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 389.3
  • LogP ≤ 5 0.22
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 184.8
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(\C=C\OCCN)/C(=O)O)O
InChI 
InChI=1S/C14H20N3O8P/c1-9-13(18)11(10(6-16-9)8-25-26(21,22)23)7-17-12(14(19)20)2-4-24-5-3-15/h2,4,6,18H,3,5,7-8,15H2,1H3,(H,19,20)(H2,21,22,23)/b4-2+,17-12+
InChIKey 
OBCQKAZQAHYUOZ-CALQLVRRSA-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 VK055_4046.

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)