Ligand profile

RED

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

Bound to: KP13_31803 — glycine cleavage system aminomethyltransferase T

Via homolog PDB 1wor UniProt Q9WY54 Formula C₈H₁₆O₂S₂
Mol. weight 208.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RED
PDB
1wor
UniProt (similar protein)
Q9WY54
Target protein
KP13_31803

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 208.35 Da
LogP (Crippen) 2.25
H-bond donors 3
H-bond acceptors 3
TPSA 37.30 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.88
Formula C₈H₁₆O₂S₂

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 37.3
  • −1 ≤ LogP ≤ 5 2.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 208.3
  • LogP ≤ 5 2.25
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 37.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCC(=O)O)C[C@H](CCS)S
InChI 
InChI=1S/C8H16O2S2/c9-8(10)4-2-1-3-7(12)5-6-11/h7,11-12H,1-6H2,(H,9,10)/t7-/m1/s1
InChIKey 
IZFHEQBZOYJLPK-SSDOTTSWSA-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
PF01571

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_31803.

PDB 4

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)