Ligand profile

5PA

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

Bound to: VK055_0027 — D-cysteine desulfhydrase monomer

Via homolog PDB 1j0b UniProt O57809 Formula C₁₂H₁₇N₂O₇P
Mol. weight 332.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5PA
PDB
1j0b
UniProt (similar protein)
O57809
Target protein
VK055_0027

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 332.25 Da
LogP (Crippen) 0.41
H-bond donors 5
H-bond acceptors 6
TPSA 149.21 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₂O₇P

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 0.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 332.2
  • LogP ≤ 5 0.41
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 149.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNC2(CC2)C(=O)O)O
InChI 
InChI=1S/C12H17N2O7P/c1-7-10(15)9(5-14-12(2-3-12)11(16)17)8(4-13-7)6-21-22(18,19)20/h4,14-15H,2-3,5-6H2,1H3,(H,16,17)(H2,18,19,20)
InChIKey 
ZMHRUAWWUAOOQN-UHFFFAOYSA-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
PF00291

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_0027.

PDB 9

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

Ligand PDB entry

ZINC 24

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

Compound Similarity (Tanimoto)