Ligand profile

D8Z

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

Bound to: VK055_2565 — molybdopterin adenylyltransferase

Via homolog PDB 6fgd UniProt Q03555 Formula C₁₆H₂₆O₅
Mol. weight 298.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D8Z
PDB
6fgd
UniProt (similar protein)
Q03555
Target protein
VK055_2565

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 298.38 Da
LogP (Crippen) 2.84
H-bond donors 0
H-bond acceptors 5
TPSA 46.15 Ų
Rotatable bonds 1
Aromatic rings 0 / 5
Heavy atoms 21
Fraction sp³ C 1.00
Formula C₁₆H₂₆O₅

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 46.2
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 298.4
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 46.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CC[C@H]2[C@H]([C@H](O[C@H]3[C@@]24[C@H]1CC[C@](O3)(OO4)C)OC)C
InChI 
InChI=1S/C16H26O5/c1-9-5-6-12-10(2)13(17-4)18-14-16(12)11(9)7-8-15(3,19-14)20-21-16/h9-14H,5-8H2,1-4H3/t9-,10-,11+,12+,13+,14-,15-,16-/m1/s1
InChIKey 
SXYIRMFQILZOAM-HVNFFKDJSA-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
PF00994' 'PF03453' '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)