Research workbench
Crystal structure of bio-32546 bound mouse autotaxin
Analyse Crystal structure of bio-32546 bound mouse autotaxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MFH
- Type
- protein
- Length
- 776 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
- Q9R1E6
- Ligands
- ZF7, NAG, MAN, BMA, ZN, IOD
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 776 | 29% helix, 19% strand | Q9R1E6 |
Ligands and binding sites
- ZF7 · (1R,3S,5S)-8-{(1S)-1-[8-(trifluoromethyl)-7-{[(1s,4R)-4-(trifluoromethyl)cyclohexyl]oxy}naphthalen-2-yl]ethyl}-8-azabicyclo[3.2.1]octane-3-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 7 copies · chains A
- IOD · Iodide ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.77 | 0.79 | 75 | ZF7, EDO, ZN |
| 2 | 253 | 0.61 | 0.80 | 38 | EDO |
| 3 | 301 | 0.58 | 0.77 | 29 | empty |
| 4 | 193 | 0.55 | 0.79 | 31 | empty |
| 5 | 139 | 0.46 | 0.77 | 26 | empty |
Modifications
Observed in the structure: 15 disulfide, 3 covalent, 2 glycan (disulfide, additive adduct, N-glycosylation).
Compared structures
- 7MFH · Crystal structure of BIO-32546 bound mouse Autotaxin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R1E6 · AlphaFold monomer V2.0 prediction for ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9R1E6
- Elsewhere: RCSB PDB 7MFH · PDBe 7MFH · UniProt Q9R1E6
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