Ligand profile

Y2A

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

Bound to: VK055_1793 — succinyl-CoA synthetase, alpha subunit

Via homolog PDB 7liw UniProt P53396 Formula C₆H₉O₁₀P
Mol. weight 272.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y2A
PDB
7liw
UniProt (similar protein)
P53396
Target protein
VK055_1793

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 272.10 Da
LogP (Crippen) -1.70
H-bond donors 5
H-bond acceptors 6
TPSA 178.66 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.50
Formula C₆H₉O₁₀P

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 178.7
  • −1 ≤ LogP ≤ 5 -1.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 272.1
  • LogP ≤ 5 -1.70
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 178.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)O)[C@](CC(=O)OP(=O)(O)O)(C(=O)O)O
InChI 
InChI=1S/C6H9O10P/c7-3(8)1-6(12,5(10)11)2-4(9)16-17(13,14)15/h12H,1-2H2,(H,7,8)(H,10,11)(H2,13,14,15)/t6-/m0/s1
InChIKey 
RAAPFOXFYNTKEB-LURJTMIESA-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
PF00549' 'PF16114

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_1793.

PDB 11

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

Ligand PDB entry

ChEMBL 56

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)