Ligand profile

41N

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

Bound to: VK055_1732 — adenosylmethionine-8-amino-7-oxononanoate transaminase

Via homolog PDB 4xjp UniProt P9WQ81 Formula C₂₀H₂₀N₂O₄
Mol. weight 352.39 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
41N
PDB
4xjp
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 352.39 Da
LogP (Crippen) 2.58
H-bond donors 0
H-bond acceptors 5
TPSA 59.08 Ų
Rotatable bonds 3
Aromatic rings 2 / 4
Heavy atoms 26
Fraction sp³ C 0.30
Formula C₂₀H₂₀N₂O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 59.1
  • −1 ≤ LogP ≤ 5 2.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 352.4
  • LogP ≤ 5 2.58
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 59.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3ccc4c(c3)OCO4
InChI 
InChI=1S/C20H20N2O4/c1-14(23)15-2-5-17(6-3-15)21-8-10-22(11-9-21)20(24)16-4-7-18-19(12-16)26-13-25-18/h2-7,12H,8-11,13H2,1H3
InChIKey 
DMJGPASMZSNEAZ-UHFFFAOYSA-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
PF00202

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_1732.

PDB 25

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)