Ligand profile

ZINC1319000

Virtual-screening candidate from ZINC.

Bound to: VK055_3627 — 4-amino-4-deoxy-L-arabinose (L-Ara4N) transferase

Via homolog UniProt O52327 Formula C₁₃H₁₈O₉
Tanimoto 0.56
Mol. weight 318.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1319000
UniProt (similar protein)
O52327
Tanimoto
0.556
Target protein
VK055_3627

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.28 Da
LogP (Crippen) -0.30
H-bond donors 0
H-bond acceptors 9
TPSA 114.43 Ų
Rotatable bonds 4
Aromatic rings 0 / 1
Heavy atoms 22
Fraction sp³ C 0.69
Formula C₁₃H₁₈O₉

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 114.4
  • −1 ≤ LogP ≤ 5 -0.30
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 318.3
  • LogP ≤ 5 -0.30
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 114.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)O[C@@H]1OC[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@H]1OC(C)=O
InChI 
InChI=1S/C13H18O9/c1-6(14)19-10-5-18-13(22-9(4)17)12(21-8(3)16)11(10)20-7(2)15/h10-13H,5H2,1-4H3/t10-,11+,12-,13+/m1/s1
InChIKey 
MJOQJPYNENPSSS-XQHKEYJVSA-N

Provenance

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

Method
LigQ nearest_k
Query
CHEMBL255766
Homolog
O52327

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_3627.

PDB 4

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)