Ligand profile

FOR

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

Bound to: KP13_04436 — hypothetical protein

Via homolog PDB 5lbm UniProt Q8X5J3 Formula CH₂O
Mol. weight 30.03 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FOR
PDB
5lbm
UniProt (similar protein)
Q8X5J3
Target protein
KP13_04436

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 30.03 Da
LogP (Crippen) -0.18
H-bond donors 0
H-bond acceptors 1
TPSA 17.07 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 2
Fraction sp³ C 0.00
Formula CH₂O

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 -0.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 30.0
  • LogP ≤ 5 -0.18
  • 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 
C=O
InChI 
InChI=1S/CH2O/c1-2/h1H2
InChIKey 
WSFSSNUMVMOOMR-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
PF02583

External resources

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