Crystal structure of KPT276 in complex with CRM1-ran-RANBP1

Structure

x-ray diffraction · 3 distinct chains · 65% helix, 8% strand (DSSP).

Ligands and binding sites

• GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
• K76 · (2E)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-1-(3,3-difluoroazetidin-1-yl)prop-2-en-1-one · ligand · chains C
• MG · Magnesium ion · metal · chains A
• CL · Chloride ion · ion · 3 copies · chains C, A
• GOL · Glycerol · additive · 4 copies · chains A, C
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 2266 Ų buried · 32 hydrogen bonds · protein-protein
• A–B · 2135 Ų buried · 37 hydrogen bonds · protein-protein
• B–C · 253 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 4WVF · Crystal structure of KPT276 in complex with CRM1-Ran-RanBP1 · the same entry in another collection · chain A against A, TM-score 1.00
• P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P62826
• Every structure of UniProt P41920
• Every structure of UniProt W7PTE1
• Elsewhere: RCSB PDB 4WVF · PDBe 4WVF · UniProt P62826 · UniProt P41920 · UniProt W7PTE1