Ligand profile

ZINC1319874

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₅H₂₃N₅O₅
Tanimoto 0.63
Mol. weight 353.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1319874
UniProt (similar protein)
P07884
Tanimoto
0.631
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 353.38 Da
LogP (Crippen) -1.13
H-bond donors 5
H-bond acceptors 10
TPSA 145.78 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.67
Formula C₁₅H₂₃N₅O₅

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 145.8
  • −1 ≤ LogP ≤ 5 -1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 353.4
  • LogP ≤ 5 -1.13
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 145.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](CO)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C15H23N5O5/c1-8(4-21)2-3-16-13-10-14(18-6-17-13)20(7-19-10)15-12(24)11(23)9(5-22)25-15/h6-9,11-12,15,21-24H,2-5H2,1H3,(H,16,17,18)/t8-,9+,11+,12+,15+/m0/s1
InChIKey 
DBVVQDGIJAUEAZ-OPYVMVOTSA-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)