Ligand profile

Y02

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 3pka UniProt P9WK19 Formula C₂₃H₃₇NO₆
Mol. weight 423.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y02
PDB
3pka
UniProt (similar protein)
P9WK19
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.55 Da
LogP (Crippen) 1.81
H-bond donors 4
H-bond acceptors 6
TPSA 108.25 Ų
Rotatable bonds 10
Aromatic rings 1 / 1
Heavy atoms 30
Fraction sp³ C 0.61
Formula C₂₃H₃₇NO₆

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 108.3
  • −1 ≤ LogP ≤ 5 1.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 423.6
  • LogP ≤ 5 1.81
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 108.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(c(c(c1)C)OCCNC(=O)[C@@H]([C@@H]([C@H]([C@@H](/C=C/C(C)(C)C)O)O)O)OC)C
InChI 
InChI=1S/C23H37NO6/c1-14-12-15(2)20(16(3)13-14)30-11-10-24-22(28)21(29-7)19(27)18(26)17(25)8-9-23(4,5)6/h8-9,12-13,17-19,21,25-27H,10-11H2,1-7H3,(H,24,28)/b9-8+/t17-,18+,19-,21-/m1/s1
InChIKey 
UMRMEUOEFMNZRM-SWQIVCBNSA-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)