Ligand profile

Y16

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 3pkb UniProt P9WK19 Formula C₁₄H₂₆N₂O₆
Mol. weight 318.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y16
PDB
3pkb
UniProt (similar protein)
P9WK19
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.37 Da
LogP (Crippen) -1.71
H-bond donors 5
H-bond acceptors 6
TPSA 142.11 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 22
Fraction sp³ C 0.71
Formula C₁₄H₂₆N₂O₆

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 142.1
  • −1 ≤ LogP ≤ 5 -1.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 318.4
  • LogP ≤ 5 -1.71
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 142.1
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)NCC(=O)N)OC)O)O)O
InChI 
InChI=1S/C14H26N2O6/c1-14(2,3)6-5-8(17)10(19)11(20)12(22-4)13(21)16-7-9(15)18/h5-6,8,10-12,17,19-20H,7H2,1-4H3,(H2,15,18)(H,16,21)/b6-5+/t8-,10+,11-,12-/m1/s1
InChIKey 
AVLHKXXFCITIMH-JXTMJACFSA-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)