Ligand profile

ZINC13516496

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₁H₁₆N₅O₇P
Tanimoto 0.75
Mol. weight 361.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13516496
UniProt (similar protein)
P07884
Tanimoto
0.750
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 361.25 Da
LogP (Crippen) -1.40
H-bond donors 5
H-bond acceptors 10
TPSA 172.08 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.55
Formula C₁₁H₁₆N₅O₇P

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 -1.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 361.3
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 172.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C11H16N5O7P/c1-12-9-6-10(14-3-13-9)16(4-15-6)11-8(18)7(17)5(23-11)2-22-24(19,20)21/h3-5,7-8,11,17-18H,2H2,1H3,(H,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKey 
WETVNPRPZIYMAC-IOSLPCCCSA-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)