Ligand profile

ZINC5412158

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₇H₂₀N₅O₇P
Tanimoto 0.70
Mol. weight 437.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5412158
UniProt (similar protein)
P07884
Tanimoto
0.697
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.35 Da
LogP (Crippen) 0.17
H-bond donors 5
H-bond acceptors 10
TPSA 172.08 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.35
Formula C₁₇H₂₀N₅O₇P

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 172.1
  • −1 ≤ LogP ≤ 5 0.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.3
  • LogP ≤ 5 0.17
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 172.1
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(NCc4ccccc4)ncnc32)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C17H20N5O7P/c23-13-11(7-28-30(25,26)27)29-17(14(13)24)22-9-21-12-15(19-8-20-16(12)22)18-6-10-4-2-1-3-5-10/h1-5,8-9,11,13-14,17,23-24H,6-7H2,(H,18,19,20)(H2,25,26,27)/t11-,13+,14-,17+/m0/s1
InChIKey 
DWVANBHPEPSMOV-XZBIERFOSA-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)