Ligand profile

Y08

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 3pkc UniProt P9WK19 Formula C₂₂H₃₈N₂O₆
Mol. weight 426.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y08
PDB
3pkc
UniProt (similar protein)
P9WK19
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.55 Da
LogP (Crippen) 0.45
H-bond donors 4
H-bond acceptors 6
TPSA 119.33 Ų
Rotatable bonds 9
Aromatic rings 0 / 2
Heavy atoms 30
Fraction sp³ C 0.82
Formula C₂₂H₃₈N₂O₆

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 119.3
  • −1 ≤ LogP ≤ 5 0.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.6
  • LogP ≤ 5 0.45
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 119.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NC[C@@H]1CCCN(C1)C(=O)C2CC2)OC)O)O)O
InChI 
InChI=1S/C22H38N2O6/c1-22(2,3)10-9-16(25)17(26)18(27)19(30-4)20(28)23-12-14-6-5-11-24(13-14)21(29)15-7-8-15/h9-10,14-19,25-27H,5-8,11-13H2,1-4H3,(H,23,28)/b10-9+/t14-,16+,17-,18+,19+/m0/s1
InChIKey 
JFNUXOSYQRHRBI-NNURDPEKSA-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
PF00557

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_2384.

PDB 45

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)