Ligand profile

ZINC124645494

Virtual-screening candidate from ZINC.

Bound to: VK055_1328 — cupin superfamily protein

Via homolog UniProt Q9H6W3 Formula C₁₃H₁₆N₂O₄
Tanimoto 0.55
Mol. weight 264.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC124645494
UniProt (similar protein)
Q9H6W3
Tanimoto
0.553
Target protein
VK055_1328

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 264.28 Da
LogP (Crippen) 0.81
H-bond donors 3
H-bond acceptors 4
TPSA 99.52 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.46
Formula C₁₃H₁₆N₂O₄

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 99.5
  • −1 ≤ LogP ≤ 5 0.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 264.3
  • LogP ≤ 5 0.81
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 99.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(N[C@H]1CCCC[C@H]1O)c1ccnc(C(=O)O)c1
InChI 
InChI=1S/C13H16N2O4/c16-11-4-2-1-3-9(11)15-12(17)8-5-6-14-10(7-8)13(18)19/h5-7,9,11,16H,1-4H2,(H,15,17)(H,18,19)/t9-,11+/m0/s1
InChIKey 
WPJAQKSBWYQNNE-GXSJLCMTSA-N

Provenance

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

Method
LigQ nearest_k
Query
PD2
Homolog
Q9H6W3

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_1328.

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)