Ligand profile

2ME

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

Bound to: KP13_01374 — NADH pyrophosphatase

Via homolog PDB 5wwd UniProt Q9CA40 Formula C₃H₈O
Mol. weight 60.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2ME
PDB
5wwd
UniProt (similar protein)
Q9CA40
Target protein
KP13_01374

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 60.10 Da
LogP (Crippen) 0.65
H-bond donors 0
H-bond acceptors 1
TPSA 9.23 Ų
Rotatable bonds 1
Aromatic rings 0 / 0
Heavy atoms 4
Fraction sp³ C 1.00
Formula C₃H₈O

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 9.2
  • −1 ≤ LogP ≤ 5 0.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 60.1
  • LogP ≤ 5 0.65
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 9.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOC
InChI 
InChI=1S/C3H8O/c1-3-4-2/h3H2,1-2H3
InChIKey 
XOBKSJJDNFUZPF-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
PF00293

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_01374.

PDB 6

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)