Ligand profile

Y10

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 3pkd UniProt P9WK19 Formula C₂₁H₃₁NO₅
Mol. weight 377.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y10
PDB
3pkd
UniProt (similar protein)
P9WK19
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 377.48 Da
LogP (Crippen) 0.97
H-bond donors 4
H-bond acceptors 5
TPSA 99.02 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.57
Formula C₂₁H₃₁NO₅

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 99.0
  • −1 ≤ LogP ≤ 5 0.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 377.5
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 99.0
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)NC1Cc2ccccc2C1)OC)O)O)O
InChI 
InChI=1S/C21H31NO5/c1-21(2,3)10-9-16(23)17(24)18(25)19(27-4)20(26)22-15-11-13-7-5-6-8-14(13)12-15/h5-10,15-19,23-25H,11-12H2,1-4H3,(H,22,26)/b10-9+/t16-,17+,18-,19-/m1/s1
InChIKey 
XTHOIFAGDPGJPZ-PQQJDVFMSA-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)