Research workbench
Evaluation of synthetic FK506 analogs as ligands for FKBP51 and FKBP52: complex of FKBP51 with {3-[(1R)-3-(3,4-dimethoxyphenyl)-1- ({[(2S)-1-(3,3-dimethyl-2-OXOPENTANOYL)PIPERIDIN-2-YL]CARBONYL}OXY) PROPYL]PHENOXY}ACETIC acid
Analyse Evaluation of synthetic FK506 analogs as ligands for FKBP51 and FKBP52: complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DRK
- Type
- protein
- Length
- 255 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase FKBP5
- EC
- 5.2.1.8
- UniProt
- Q13451
- Ligands
- I63
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase FKBP5 (EC 5.2.1.8) | protein | 128 | 17% helix, 38% strand | Q13451 |
| B | Peptidyl-prolyl cis-trans isomerase FKBP5 (EC 5.2.1.8) | protein | 127 | 18% helix, 38% strand | Q13451 |
Ligands and binding sites
- I63 · {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-(3,3-dimethyl-2-oxopentanoyl)piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.73 | 0.80 | 40 | empty |
| 2 | 68 | 0.38 | 0.78 | 13 | I63 |
| 3 | 77 | 0.37 | 0.76 | 12 | I63 |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4DRK · EVALUATION OF SYNTHETIC FK506 ANALOGS AS LIGANDS FOR FKBP51 AND FKBP52: COMPLEX OF FKBP51… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13451 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP5 (Q13451) · a predicted model of the same protein · chain B 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 Q13451
- Elsewhere: RCSB PDB 4DRK · PDBe 4DRK · UniProt Q13451
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