Research workbench
Glucocorticoid receptor with bound D-prolinamide 11
Analyse Glucocorticoid receptor with bound D-prolinamide 11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K23
- Type
- protein
- Length
- 767 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Nuclear receptor coactivator 2
- UniProt
- P04150, Q15596
- Ligands
- JZN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 245 | 64% helix, 5% strand | P04150 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 67% helix, 0% strand | Q15596 |
| B | Glucocorticoid receptor | protein | 247 | 64% helix, 5% strand | P04150 |
| E | Nuclear receptor coactivator 2 | protein | 10 | 80% helix, 0% strand | Q15596 |
| C | Glucocorticoid receptor | protein | 246 | 60% helix, 5% strand | P04150 |
| F | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | Q15596 |
Ligands and binding sites
- JZN · 1-{[3-(4-{[(2R)-4-(5-fluoro-2-methoxyphenyl)-2-hydroxy-4-methyl-2-(trifluoromethyl)pentyl]amino}-6-methyl-1H-indazol-1-yl)phenyl]carbonyl}-D-prolinamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.85 | 0.95 | 40 | JZN |
| 2 | 978 | 0.84 | 0.85 | 82 | JZN |
| 3 | 420 | 0.84 | 0.91 | 52 | JZN |
| 4 | 132 | 0.71 | 0.91 | 28 | empty |
| 5 | 600 | 0.67 | 0.77 | 47 | empty |
Interfaces
6 interfaces between chains.
- B–C · 734 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 523 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 485 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 336 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P04150
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3K23 · PDBe 3K23 · UniProt P04150 · UniProt Q15596
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