Ligand profile

XL3

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

Bound to: KP13_00947 — Alpha-ketoglutarate-dependent dioxygenase alkB

Via homolog PDB 6ksf UniProt P0CB42 Formula C₃H₈S
Mol. weight 76.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XL3
PDB
6ksf
UniProt (similar protein)
P0CB42
Target protein
KP13_00947

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 76.16 Da
LogP (Crippen) 1.33
H-bond donors 1
H-bond acceptors 1
TPSA 0.00 Ų
Rotatable bonds 1
Aromatic rings 0 / 0
Heavy atoms 4
Fraction sp³ C 1.00
Formula C₃H₈S

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 0.0
  • −1 ≤ LogP ≤ 5 1.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 76.2
  • LogP ≤ 5 1.33
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCS
InChI 
InChI=1S/C3H8S/c1-2-3-4/h4H,2-3H2,1H3
InChIKey 
SUVIGLJNEAMWEG-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
PF13532

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_00947.

PDB 3

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

Ligand PDB entry

ChEMBL 41

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)