Ligand profile

N2P

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

Bound to: KP13_04437 — S-(hydroxymethyl)glutathione dehydrogenase

Via homolog PDB 3qj5 UniProt P11766 Formula C₅H₁₄N₂
Mol. weight 102.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
N2P
PDB
3qj5
UniProt (similar protein)
P11766
Target protein
KP13_04437

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 102.18 Da
LogP (Crippen) 0.07
H-bond donors 2
H-bond acceptors 2
TPSA 52.04 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 1.00
Formula C₅H₁₄N₂

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 52.0
  • −1 ≤ LogP ≤ 5 0.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 102.2
  • LogP ≤ 5 0.07
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 52.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCN)CCN
InChI 
InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2
InChIKey 
VHRGRCVQAFMJIZ-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
PF00107' 'PF08240

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_04437.

PDB 26

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

Ligand PDB entry

ChEMBL 16

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)