Ligand profile

ZINC77312680

Virtual-screening candidate from ZINC.

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog UniProt P0CE48 Formula C₉H₁₅N₂O₁₅P₃
Tanimoto 0.81
Mol. weight 484.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC77312680
UniProt (similar protein)
P0CE48
Tanimoto
0.812
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.14 Da
LogP (Crippen) -2.43
H-bond donors 8
H-bond acceptors 11
TPSA 275.23 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.56
Formula C₉H₁₅N₂O₁₅P₃

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 275.2
  • −1 ≤ LogP ≤ 5 -2.43
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 484.1
  • LogP ≤ 5 -2.43
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 275.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1[nH]cc([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C9H15N2O15P3/c12-5-4(2-23-28(19,20)26-29(21,22)25-27(16,17)18)24-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H,19,20)(H,21,22)(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
InChIKey 
VEWJOCYCKIZKKV-GBNDHIKLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
PSU
Homolog
P0CE48

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_3750.

PDB 20

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)