Ligand profile

QYD

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_0681 — alpha/beta hydrolase fold family protein

Via homolog PDB 5alp UniProt P34913 Formula C₁₇H₁₇N₃O₃S
Mol. weight 343.41 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
QYD
PDB
5alp
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 343.41 Da
LogP (Crippen) 3.92
H-bond donors 1
H-bond acceptors 4
TPSA 75.48 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.24
Formula C₁₇H₁₇N₃O₃S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 75.5
  • −1 ≤ LogP ≤ 5 3.92
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 343.4
  • LogP ≤ 5 3.92
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 75.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)[C@H]2CN(CCS2)C(=O)Nc3ccc(cc3)[N+](=O)[O-]
InChI 
InChI=1S/C17H17N3O3S/c21-17(18-14-6-8-15(9-7-14)20(22)23)19-10-11-24-16(12-19)13-4-2-1-3-5-13/h1-9,16H,10-12H2,(H,18,21)/t16-/m1/s1
InChIKey 
PNYRURHCCDDZLP-MRXNPFEDSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00561

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_0681.

PDB 98

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)