MolNFT v1 · #99769 · protein
Crystal structure of the glucocorticoid receptor bound to a non- steroidal antagonist reveals repositioning and partial disordering of activation function helix 12
4MDD: “Crystal structure of the glucocorticoid receptor bound to a non- steroidal antagonist reveals repositioning…”. X-ray diffraction, 1 ligand (29M), 5 pockets (best druggability 0.76). MolNFT v1 #99769 on GenesisL1: 3D structure…
- PDB
- 4MDD
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Nuclear receptor corepressor 1
- UniProt
- P04150, O75376
- Ligands
- 29M
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 247 | 66% helix, 5% strand | P04150 |
| B | Glucocorticoid receptor | protein | 220 | 68% helix, 6% strand | P04150 |
| C | Nuclear receptor corepressor 1 | protein | 13 | 85% helix, 0% strand | O75376 |
| D | Nuclear receptor corepressor 1 | protein | 12 | 83% helix, 0% strand | O75376 |
Ligands and binding sites
- 29M · N-[2-{[benzyl(methyl)amino]methyl}-3-(4-fluoro-2-methoxyphenyl)-5-(propan-2-yl)-1H-indol-7-yl]methanesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.76 | 0.78 | 78 | 29M |
| 2 | 495 | 0.75 | 0.82 | 49 | 29M |
| 3 | 167 | 0.67 | 0.87 | 24 | empty |
| 4 | 138 | 0.66 | 0.87 | 20 | empty |
| 5 | 58 | 0.31 | 0.75 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2581 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 522 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 38 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4MDD · Crystal Structure of the Glucocorticoid Receptor Bound to a Non-steroidal Antagonist… · the same entry in another collection · chain D against D, TM-score 1.00
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain B against A, TM-score 0.87
- O75376 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 1 (O75376) · a predicted model of the same protein · chain D against A, TM-score 0.77
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 O75376
- Elsewhere: RCSB PDB 4MDD · PDBe 4MDD · UniProt P04150 · UniProt O75376
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.