Research workbench
Crystal structure of autotaxin (ENPP2) in complex with the HA155 boronic acid inhibitor
Analyse Crystal structure of autotaxin (ENPP2) in complex with the HA155 boronic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XRG
- Type
- protein
- Length
- 758 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
- SWH, NAG, BMA, ZN, CA, IOD
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ectonucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE family member 2 (EC 3.1.4.39) | protein | 758 | 26% helix, 19% strand | Q64610 |
Ligands and binding sites
- SWH · {4-[(4-{(Z)-[3-(4-fluorobenzyl)-2,4-dioxo-1,3-thiazolidin-5-ylidene]methyl}phenoxy)methyl]phenyl}(trihydroxy)borate(1-) · 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
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.77 | 0.80 | 64 | SWH, ZN, IOD |
| 2 | 55 | 0.68 | 0.96 | 15 | empty |
| 3 | 337 | 0.65 | 0.80 | 45 | empty |
| 4 | 148 | 0.64 | 0.86 | 25 | empty |
| 5 | 347 | 0.59 | 0.77 | 32 | empty |
Modifications
Observed in the structure: 14 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 2XRG · Crystal structure of Autotaxin (ENPP2) in complex with the HA155 boronic acid inhibitor · 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 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 Q64610
- Elsewhere: RCSB PDB 2XRG · PDBe 2XRG · UniProt Q64610
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