Ligand profile

ZINC59201305

Virtual-screening candidate from ZINC.

Bound to: VK055_0207 — peptidyl-tRNA hydrolase

Via homolog UniProt D0C9L6 Formula C₉H₁₂FN₃O₄
Tanimoto 0.81
Mol. weight 245.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59201305
UniProt (similar protein)
D0C9L6
Tanimoto
0.810
Target protein
VK055_0207

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 245.21 Da
LogP (Crippen) -1.59
H-bond donors 3
H-bond acceptors 7
TPSA 110.60 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.56
Formula C₉H₁₂FN₃O₄

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 110.6
  • −1 ≤ LogP ≤ 5 -1.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 245.2
  • LogP ≤ 5 -1.59
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 110.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)n1
InChI 
InChI=1S/C9H12FN3O4/c10-6-7(15)4(3-14)17-8(6)13-2-1-5(11)12-9(13)16/h1-2,4,6-8,14-15H,3H2,(H2,11,12,16)/t4-,6+,7+,8-/m1/s1
InChIKey 
NVZFZMCNALTPBY-YDKYIBAVSA-N

Provenance

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

Method
LigQ nearest_k
Query
AR3
Homolog
D0C9L6

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)