Ligand profile

6SR

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

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

Via homolog PDB 5kgs UniProt P0A4X7 Formula C₂₁H₂₀N₂O₄
Mol. weight 364.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6SR
PDB
5kgs
UniProt (similar protein)
P0A4X7
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 364.40 Da
LogP (Crippen) 2.51
H-bond donors 0
H-bond acceptors 5
TPSA 59.08 Ų
Rotatable bonds 2
Aromatic rings 2 / 5
Heavy atoms 27
Fraction sp³ C 0.33
Formula C₂₁H₂₀N₂O₄

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 2.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 364.4
  • LogP ≤ 5 2.51
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 59.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1C(=O)N3CCN(CC3)c4ccc5c(c4)CCC5=O)OCO2
InChI 
InChI=1S/C21H20N2O4/c24-18-5-1-14-11-16(3-4-17(14)18)22-7-9-23(10-8-22)21(25)15-2-6-19-20(12-15)27-13-26-19/h2-4,6,11-12H,1,5,7-10,13H2
InChIKey 
JAFWBQRYWNPFPG-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)