Research workbench
Crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5- (3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2- (pyrrolidin-1-YLSULFONYL)ETHYL]-3-methyl-2-oxopiperidin-3-YL}ACETIC acid
Analyse Crystal structure of compound 16 bound to MDM2(17-111), {(3R,5R,6S)-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QOC
- Type
- protein
- Length
- 561 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 35T
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 92 | 48% helix, 17% strand | Q00987 |
| E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 45% helix, 17% strand | Q00987 |
| G | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 44% helix, 16% strand | Q00987 |
| I | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 44% helix, 17% strand | Q00987 |
| K | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 95 | 44% helix, 16% strand | Q00987 |
Ligands and binding sites
- 35T · {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid · ligand · 6 copies · chains A, C, G, E, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.69 | 0.79 | 56 | 35T |
| 2 | 362 | 0.65 | 0.79 | 26 | 35T |
| 3 | 178 | 0.63 | 0.84 | 36 | empty |
| 4 | 187 | 0.52 | 0.78 | 37 | empty |
| 5 | 143 | 0.51 | 0.78 | 18 | 35T |
Interfaces
9 interfaces between chains.
- C–G · 591 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 581 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 11 hydrogen bonds · protein-protein
- E–K · 375 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 303 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QOC · crystal structure of compound 16 bound to MDM2(17-111)… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q00987
- Elsewhere: RCSB PDB 4QOC · PDBe 4QOC · UniProt Q00987
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