Ligand profile

KSW

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

Bound to: VK055_0488 — pentaerythritol tetranitrate reductase

Via homolog PDB 6s23 UniProt M2XAQ9 Formula C₆H₆O
Mol. weight 94.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KSW
PDB
6s23
UniProt (similar protein)
M2XAQ9
Target protein
VK055_0488

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 94.11 Da
LogP (Crippen) 1.07
H-bond donors 0
H-bond acceptors 1
TPSA 17.07 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 7
Fraction sp³ C 0.17
Formula C₆H₆O

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 17.1
  • −1 ≤ LogP ≤ 5 1.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 94.1
  • LogP ≤ 5 1.07
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 17.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=CC=CC1=O
InChI 
InChI=1S/C6H6O/c1-5-3-2-4-6(5)7/h2-4H,1H3
InChIKey 
LYYZLRGLZHSYLN-UHFFFAOYSA-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
PF00724

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_0488.

PDB 19

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)