Ligand profile

40N

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

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

Via homolog PDB 4xew UniProt P9WQ81 Formula C₁₆H₁₀FNO₃
Mol. weight 283.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
40N
PDB
4xew
UniProt (similar protein)
P9WQ81
Target protein
VK055_1732

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 283.26 Da
LogP (Crippen) 3.06
H-bond donors 1
H-bond acceptors 3
TPSA 51.32 Ų
Rotatable bonds 1
Aromatic rings 3 / 4
Heavy atoms 21
Fraction sp³ C 0.06
Formula C₁₆H₁₀FNO₃

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 51.3
  • −1 ≤ LogP ≤ 5 3.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 283.3
  • LogP ≤ 5 3.06
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 51.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)C2=CC(=O)c3cc4c(cc3N2)OCO4)F
InChI 
InChI=1S/C16H10FNO3/c17-11-4-2-1-3-9(11)12-6-14(19)10-5-15-16(21-8-20-15)7-13(10)18-12/h1-7H,8H2,(H,18,19)
InChIKey 
ZMYDAPJHGNEFGQ-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)