Ligand profile

ZINC5439578

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₅H₂₂N₅O₇P
Tanimoto 0.73
Mol. weight 415.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5439578
UniProt (similar protein)
P07884
Tanimoto
0.734
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.34 Da
LogP (Crippen) -0.07
H-bond donors 5
H-bond acceptors 10
TPSA 172.08 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.53
Formula C₁₅H₂₂N₅O₇P

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 -0.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 415.3
  • LogP ≤ 5 -0.07
  • 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 
CC(C)=CCNc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C15H22N5O7P/c1-8(2)3-4-16-13-10-14(18-6-17-13)20(7-19-10)15-12(22)11(21)9(27-15)5-26-28(23,24)25/h3,6-7,9,11-12,15,21-22H,4-5H2,1-2H3,(H,16,17,18)(H2,23,24,25)/t9-,11+,12+,15-/m0/s1
InChIKey 
DUISZFLWBAPRBR-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)