Research workbench
Structure-based evolution of a hybrid steroid series of autotaxin inhibitors
Analyse Structure-based evolution of a hybrid steroid series of autotaxin inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M0E
- Type
- protein
- Length
- 772 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2
- EC
- 3.1.4.39
- UniProt
- Q64610
- Ligands
- 5JK, 7CR, NAG, BMA, ZN, NA, CA, SCN, IOD
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 772 | 30% helix, 20% strand | Q64610 |
Ligands and binding sites
- 5JK · 7alpha-hydroxycholesterol · ligand · chains A
- 7CR · [3,5-bis(chloranyl)phenyl]methyl 4-[(3~{R})-3-oxidanyl-3-(2-oxidanylidene-3~{H}-1,3-benzoxazol-6-yl) propyl]piperazine-1-carboxylate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 17 copies · chains A
- IOD · Iodide ion · ion · 14 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.74 | 0.78 | 80 | ZN, IOD, 5JK, 7CR, SCN |
| 2 | 277 | 0.60 | 0.79 | 30 | empty |
| 3 | 200 | 0.57 | 0.80 | 32 | empty |
| 4 | 178 | 0.53 | 0.79 | 31 | IOD |
| 5 | 102 | 0.50 | 0.82 | 16 | empty |
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5M0E · Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q64610 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q64610
- Elsewhere: RCSB PDB 5M0E · PDBe 5M0E · UniProt Q64610
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