Ligand profile

ZINC5432461

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₅H₁₈N₅O₈P
Tanimoto 0.68
Mol. weight 427.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5432461
UniProt (similar protein)
P07884
Tanimoto
0.676
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 427.31 Da
LogP (Crippen) -0.24
H-bond donors 5
H-bond acceptors 11
TPSA 185.22 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.40
Formula C₁₅H₁₈N₅O₈P

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 185.2
  • −1 ≤ LogP ≤ 5 -0.24
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 427.3
  • LogP ≤ 5 -0.24
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 185.2
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(NCc4ccco4)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C15H18N5O8P/c21-11-9(5-27-29(23,24)25)28-15(12(11)22)20-7-19-10-13(17-6-18-14(10)20)16-4-8-2-1-3-26-8/h1-3,6-7,9,11-12,15,21-22H,4-5H2,(H,16,17,18)(H2,23,24,25)/t9-,11+,12+,15-/m0/s1
InChIKey 
WDFCXEWULSQTFC-NFOTXUCKSA-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)