Ligand profile

ZINC71766855

Virtual-screening candidate from ZINC.

Bound to: VK055_1382 — ribonuclease E

Via homolog UniProt P21513 Formula C₁₃H₂₀N₃O₉P
Tanimoto 0.72
Mol. weight 393.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC71766855
UniProt (similar protein)
P21513
Tanimoto
0.717
Target protein
VK055_1382

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 393.29 Da
LogP (Crippen) -2.39
H-bond donors 4
H-bond acceptors 9
TPSA 163.55 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 26
Fraction sp³ C 0.69
Formula C₁₃H₂₀N₃O₉P

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 163.5
  • −1 ≤ LogP ≤ 5 -2.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 393.3
  • LogP ≤ 5 -2.39
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 163.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3)[C@@H](O)[C@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C13H20N3O9P/c17-9-1-2-16(13(20)14-9)12-11(19)10(18)8(25-12)7-24-26(21,22)15-3-5-23-6-4-15/h1-2,8,10-12,18-19H,3-7H2,(H,21,22)(H,14,17,20)/t8-,10-,11-,12-/m1/s1
InChIKey 
AJFNOZWHVDTKIH-HJQYOEGKSA-N

Provenance

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

Method
LigQ nearest_k
Query
U
Homolog
P21513

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_1382.

PDB 1

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)