Ligand profile

YZ6

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4fll UniProt P53582 Formula C₂₅H₃₅NO₆
Mol. weight 445.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YZ6
PDB
4fll
UniProt (similar protein)
P53582
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 445.56 Da
LogP (Crippen) 2.62
H-bond donors 4
H-bond acceptors 6
TPSA 112.16 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.48
Formula C₂₅H₃₅NO₆

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 112.2
  • −1 ≤ LogP ≤ 5 2.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 445.6
  • LogP ≤ 5 2.62
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 112.2
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[C@H](c1ccccc1)c2ccco2)OC)O)O)O
InChI 
InChI=1S/C25H35NO6/c1-25(2,3)14-12-19(27)21(28)22(29)23(31-4)24(30)26-15-13-18(20-11-8-16-32-20)17-9-6-5-7-10-17/h5-12,14,16,18-19,21-23,27-29H,13,15H2,1-4H3,(H,26,30)/b14-12+/t18-,19-,21+,22-,23-/m1/s1
InChIKey 
WQHBNFLTBJLEJU-VQDAETQCSA-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)