Ligand profile

3F8

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

Bound to: VK055_2565 — molybdopterin adenylyltransferase

Via homolog PDB 6hsn UniProt Q03555 Formula C₁₄H₁₆N₂O₆
Mol. weight 308.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3F8
PDB
6hsn
UniProt (similar protein)
Q03555
Target protein
VK055_2565

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.29 Da
LogP (Crippen) -1.13
H-bond donors 0
H-bond acceptors 6
TPSA 93.22 Ų
Rotatable bonds 9
Aromatic rings 0 / 2
Heavy atoms 22
Fraction sp³ C 0.43
Formula C₁₄H₁₆N₂O₆

Drug-likeness

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

Permeability proxy Check

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 93.2
  • −1 ≤ LogP ≤ 5 -1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 -1.13
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 93.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CC(=O)N(C1=O)CCOCCOCCN2C(=O)C=CC2=O
InChI 
InChI=1S/C14H16N2O6/c17-11-1-2-12(18)15(11)5-7-21-9-10-22-8-6-16-13(19)3-4-14(16)20/h1-4H,5-10H2
InChIKey 
FERLGYOHRKHQJP-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
PF03454

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_2565.

PDB 9

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)