Ligand profile

41F

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

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

Via homolog PDB 4xjl UniProt P9WQ81 Formula C₁₇H₁₇N₅OS
Mol. weight 339.42 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
41F
PDB
4xjl
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 339.42 Da
LogP (Crippen) 3.05
H-bond donors 1
H-bond acceptors 5
TPSA 61.36 Ų
Rotatable bonds 2
Aromatic rings 3 / 4
Heavy atoms 24
Fraction sp³ C 0.24
Formula C₁₇H₁₇N₅OS

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 61.4
  • −1 ≤ LogP ≤ 5 3.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 339.4
  • LogP ≤ 5 3.05
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 61.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)N2CCN(CC2)C(=O)Nc3ccc4c(c3)nns4
InChI 
InChI=1S/C17H17N5OS/c23-17(18-13-6-7-16-15(12-13)19-20-24-16)22-10-8-21(9-11-22)14-4-2-1-3-5-14/h1-7,12H,8-11H2,(H,18,23)
InChIKey 
FFLVDHOMQBCRBY-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)