Ligand profile

3GN

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

Bound to: VK055_3566 — ankyrin repeat family protein

Via homolog PDB 4tjy UniProt Q9H2K2 Formula C₁₃H₁₆N₄O
Mol. weight 244.30 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3GN
PDB
4tjy
UniProt (similar protein)
Q9H2K2
Target protein
VK055_3566

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 244.30 Da
LogP (Crippen) 1.26
H-bond donors 3
H-bond acceptors 3
TPSA 83.80 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.38
Formula C₁₃H₁₆N₄O

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 83.8
  • −1 ≤ LogP ≤ 5 1.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 244.3
  • LogP ≤ 5 1.26
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 83.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]1(CCCN1)c2[nH]c3c(cccc3n2)C(=O)N
InChI 
InChI=1S/C13H16N4O/c1-13(6-3-7-15-13)12-16-9-5-2-4-8(11(14)18)10(9)17-12/h2,4-5,15H,3,6-7H2,1H3,(H2,14,18)(H,16,17)/t13-/m0/s1
InChIKey 
JNAHVYVRKWKWKQ-ZDUSSCGKSA-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
PF00644

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_3566.

PDB 124

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

Ligand PDB entry

ChEMBL 100

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)