Ligand profile

ZINC4096207

Virtual-screening candidate from ZINC.

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog UniProt P07884 Formula C₁₄H₁₈N₅O₁₁P
Tanimoto 0.67
Mol. weight 463.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4096207
UniProt (similar protein)
P07884
Tanimoto
0.672
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 463.30 Da
LogP (Crippen) -2.11
H-bond donors 7
H-bond acceptors 12
TPSA 246.68 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₄H₁₈N₅O₁₁P

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 246.7
  • −1 ≤ LogP ≤ 5 -2.11
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 463.3
  • LogP ≤ 5 -2.11
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 246.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)C[C@H](Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]1O)C(=O)O
InChI 
InChI=1S/C14H18N5O11P/c20-7(21)1-5(14(24)25)18-11-8-12(16-3-15-11)19(4-17-8)13-10(23)9(22)6(30-13)2-29-31(26,27)28/h3-6,9-10,13,22-23H,1-2H2,(H,20,21)(H,24,25)(H,15,16,18)(H2,26,27,28)/t5-,6+,9+,10+,13+/m0/s1
InChIKey 
OFBHPPMPBOJXRT-VWJPMABRSA-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)