Ligand profile

41E

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

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

Via homolog PDB 4xjm UniProt P9WQ81 Formula C₂₂H₂₆N₂O₄S
Mol. weight 414.53 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
41E
PDB
4xjm
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 414.53 Da
LogP (Crippen) 4.23
H-bond donors 1
H-bond acceptors 5
TPSA 75.71 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.41
Formula C₂₂H₂₆N₂O₄S

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 75.7
  • −1 ≤ LogP ≤ 5 4.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 414.5
  • LogP ≤ 5 4.23
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 75.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)c1ccc(s1)C(=O)N2CCC(CC2)CCC(=O)Nc3cccc(c3)OC
InChI 
InChI=1S/C22H26N2O4S/c1-15(25)19-7-8-20(29-19)22(27)24-12-10-16(11-13-24)6-9-21(26)23-17-4-3-5-18(14-17)28-2/h3-5,7-8,14,16H,6,9-13H2,1-2H3,(H,23,26)
InChIKey 
OBNZBEYJKWRWKQ-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)