Ligand profile

GNR

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 1s17 UniProt Q9I7A8 Formula C₁₀H₁₀N₂O₃S
Mol. weight 238.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GNR
PDB
1s17
UniProt (similar protein)
Q9I7A8
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 238.27 Da
LogP (Crippen) 0.99
H-bond donors 3
H-bond acceptors 4
TPSA 78.43 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.20
Formula C₁₀H₁₀N₂O₃S

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 78.4
  • −1 ≤ LogP ≤ 5 0.99
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 238.3
  • LogP ≤ 5 0.99
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)NC(=O)[C@H](S2)CC(=O)NO
InChI 
InChI=1S/C10H10N2O3S/c13-9(12-15)5-8-10(14)11-6-3-1-2-4-7(6)16-8/h1-4,8,15H,5H2,(H,11,14)(H,12,13)/t8-/m1/s1
InChIKey 
UKDWCJNGBPZOBU-MRVPVSSYSA-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
PF01327

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_3786.

PDB 11

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)