Research workbench
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53
Analyse Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THF
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.1
- Source
- Homo sapiens
- Molecule
- Peptidyl-prolyl cis-trans isomerase F, mitochondrial
- EC
- 5.2.1.8
- UniProt
- P30405
- Ligands
- I4R
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · resolution 1.1 · 1 distinct chain · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 163 | 15% helix, 33% strand | P30405 |
Ligands and binding sites
- I4R · 3-(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)pentanedioic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.27 | 0.75 | 18 | empty |
Compared structures
- 7THF · Structure of cyclophilin D peptidyl-prolyl isomerase domain bound to macrocyclic… · the same entry in another collection · chain A against A, TM-score 1.00
- P30405 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase F… · 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 P30405
- Elsewhere: RCSB PDB 7THF · PDBe 7THF · UniProt P30405
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