Ligand profile

ZINC4824413

Virtual-screening candidate from ZINC.

Bound to: VK055_0207 — peptidyl-tRNA hydrolase

Via homolog UniProt Q9HVC3 Formula C₁₉H₂₃N₇O₄
Tanimoto 0.81
Mol. weight 413.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4824413
UniProt (similar protein)
Q9HVC3
Tanimoto
0.806
Target protein
VK055_0207

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 413.44 Da
LogP (Crippen) -1.29
H-bond donors 5
H-bond acceptors 10
TPSA 174.43 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.37
Formula C₁₉H₂₃N₇O₄

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 174.4
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 413.4
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 174.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@@H](N)Cc2ccccc2)[C@H]1O
InChI 
InChI=1S/C19H23N7O4/c20-11(6-10-4-2-1-3-5-10)18(29)25-13-12(7-27)30-19(15(13)28)26-9-24-14-16(21)22-8-23-17(14)26/h1-5,8-9,11-13,15,19,27-28H,6-7,20H2,(H,25,29)(H2,21,22,23)/t11-,12-,13+,15+,19-/m0/s1
InChIKey 
OEXKSCAXIHSIHU-ZLVSVIJZSA-N

Provenance

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

Method
LigQ nearest_k
Query
3NZ
Homolog
Q9HVC3

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_0207.

PDB 10

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)