Ligand profile

R5T

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

Bound to: VK055_4646 — aminopeptidase B

Via homolog PDB 4r6t UniProt Q8IL11 Formula C₁₆H₂₀N₄O₄
Mol. weight 332.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R5T
PDB
4r6t
UniProt (similar protein)
Q8IL11
Target protein
VK055_4646

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 332.36 Da
LogP (Crippen) 1.94
H-bond donors 3
H-bond acceptors 6
TPSA 105.48 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.31
Formula C₁₆H₂₀N₄O₄

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 105.5
  • −1 ≤ LogP ≤ 5 1.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 332.4
  • LogP ≤ 5 1.94
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 105.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)OC(=O)N[C@@H](c1ccc(cc1)n2cccn2)C(=O)NO
InChI 
InChI=1S/C16H20N4O4/c1-16(2,3)24-15(22)18-13(14(21)19-23)11-5-7-12(8-6-11)20-10-4-9-17-20/h4-10,13,23H,1-3H3,(H,18,22)(H,19,21)/t13-/m0/s1
InChIKey 
PGHJYUATTUXMSH-ZDUSSCGKSA-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
PF00883

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_4646.

PDB 9

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)