Ligand profile

KMT

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

Bound to: VK055_1890 — acireductone dioxygenase

Via homolog PDB 5i8y UniProt Q99JT9 Formula C₅H₈O₃S
Mol. weight 148.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KMT
PDB
5i8y
UniProt (similar protein)
Q99JT9
Target protein
VK055_1890

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 148.18 Da
LogP (Crippen) 0.39
H-bond donors 1
H-bond acceptors 3
TPSA 54.37 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.60
Formula C₅H₈O₃S

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 54.4
  • −1 ≤ LogP ≤ 5 0.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 148.2
  • LogP ≤ 5 0.39
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 54.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CSCCC(=O)C(=O)O
InChI 
InChI=1S/C5H8O3S/c1-9-3-2-4(6)5(7)8/h2-3H2,1H3,(H,7,8)
InChIKey 
SXFSQZDSUWACKX-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
PF03079

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_1890.

PDB 3

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)