Ligand profile

HPY

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

Bound to: VK055_3722 — amidohydrolase family protein

Via homolog PDB 1k70 UniProt P25524 Formula C₄H₆N₂O₂
Mol. weight 114.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HPY
PDB
1k70
UniProt (similar protein)
P25524
Target protein
VK055_3722

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 114.10 Da
LogP (Crippen) -0.87
H-bond donors 3
H-bond acceptors 2
TPSA 61.36 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 8
Fraction sp³ C 0.25
Formula C₄H₆N₂O₂

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 61.4
  • −1 ≤ LogP ≤ 5 -0.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 114.1
  • LogP ≤ 5 -0.87
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 61.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CNC(=O)N[C@H]1O
InChI 
InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-3,7H,(H2,5,6,8)/t3-/m0/s1
InChIKey 
DEAAWXYGBWCVJW-VKHMYHEASA-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
PF07969

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3722.

PDB 5

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

Ligand PDB entry

ZINC 4

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)