Research workbench
Crystal Structure of rat Autotaxin in complex with N-[(3-chloro-4-cyanophenyl)methyl]-2-[6-[1-(2-methoxyacetyl)piperidin-4-yl]-4-oxoquinazolin-3-yl]-N-methylacetamide, i.e. SMILES c1(ccc2c(c1)C(=O)N(C=N2)CC(=O)N(Cc1cc(c(cc1)C#N)Cl)C)C1CCN(CC1)C(=O)COC with IC50=0.0120222 microM
Analyse Crystal Structure of rat Autotaxin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7G7I
- Type
- protein
- Length
- 805 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.61
- Source
- Rattus norvegicus
- Molecule
- Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
- EC
- 3.1.4.39
- UniProt
- Q64610
- Ligands
- XRZ, MAN, NAG, BMA, CA, NA, ZN
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.61 · 1 distinct chain · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 (EC 3.1.4.39) | protein | 805 | 30% helix, 18% strand | Q64610 |
Ligands and binding sites
- XRZ · N-[(3-chloro-4-cyanophenyl)methyl]-2-{6-[1-(methoxyacetyl)piperidin-4-yl]-4-oxoquinazolin-3(4H)-yl}-N-methylacetamide · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.78 | 0.80 | 85 | XRZ |
| 2 | 242 | 0.62 | 0.81 | 27 | empty |
| 3 | 53 | 0.59 | 0.91 | 16 | empty |
| 4 | 254 | 0.58 | 0.78 | 29 | ACT |
| 5 | 286 | 0.57 | 0.77 | 48 | empty |
Modifications
Observed in the structure: 15 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 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 7G7I · PDBe 7G7I · UniProt Q64610
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