Ligand profile

ZINC2839271

Virtual-screening candidate from ZINC.

Bound to: VK055_4143 — glycine cleavage system H protein

Via homolog UniProt P16048 Formula C₁₂H₂₃NO₄
Tanimoto 0.50
Mol. weight 245.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2839271
UniProt (similar protein)
P16048
Tanimoto
0.500
Target protein
VK055_4143

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 245.32 Da
LogP (Crippen) 1.99
H-bond donors 3
H-bond acceptors 3
TPSA 100.62 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.83
Formula C₁₂H₂₃NO₄

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 100.6
  • −1 ≤ LogP ≤ 5 1.99
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 245.3
  • LogP ≤ 5 1.99
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 100.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CCCCCC(=O)O)CCCCC(=O)O
InChI 
InChI=1S/C12H23NO4/c13-10(7-4-5-9-12(16)17)6-2-1-3-8-11(14)15/h10H,1-9,13H2,(H,14,15)(H,16,17)/t10-/m0/s1
InChIKey 
XYDQDGJOQQAPIM-JTQLQIEISA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
RED
Homolog
P16048

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_4143.

PDB 3

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

Ligand PDB entry

ZINC 13

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

Compound Similarity (Tanimoto)