Ligand profile

ZINC13526959

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₀H₁₂ClN₄O₇P
Tanimoto 0.65
Mol. weight 366.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13526959
UniProt (similar protein)
P07884
Tanimoto
0.645
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 366.65 Da
LogP (Crippen) -0.79
H-bond donors 4
H-bond acceptors 9
TPSA 160.05 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₂ClN₄O₇P

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 160.1
  • −1 ≤ LogP ≤ 5 -0.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 366.7
  • LogP ≤ 5 -0.79
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 160.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=P(O)(O)OC[C@H]1O[C@@H](n2cnc3c(Cl)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C10H12ClN4O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey 
ALOBOMYIOYNCBS-KQYNXXCUSA-N

Provenance

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

Method
LigQ nearest_k
Query
6IA
Homolog
P07884

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_2895.

PDB 5

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)