Ligand profile

7A3

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

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

Via homolog PDB 5tdf UniProt P53396 Formula C₆H₈O₈
Mol. weight 208.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7A3
PDB
5tdf
UniProt (similar protein)
P53396
Target protein
VK055_1793

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 208.12 Da
LogP (Crippen) -2.28
H-bond donors 5
H-bond acceptors 5
TPSA 152.36 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.50
Formula C₆H₈O₈

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 152.4
  • −1 ≤ LogP ≤ 5 -2.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 208.1
  • LogP ≤ 5 -2.28
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 152.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)O)[C@]([C@@H](C(=O)O)O)(C(=O)O)O
InChI 
InChI=1S/C6H8O8/c7-2(8)1-6(14,5(12)13)3(9)4(10)11/h3,9,14H,1H2,(H,7,8)(H,10,11)(H,12,13)/t3-,6+/m1/s1
InChIKey 
ZMJBYMUCKBYSCP-CVYQJGLWSA-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)