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Discovery of new natural-product-inspired spiro-oxindole compounds as orally active inhibitors of the MDM2-P53 interaction: HDM2 (MDM2) in complex with compound 6G
Analyse Discovery of new natural-product-inspired spiro-oxindole compounds as orally… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LAY
- Type
- protein
- Length
- 552 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
- 6SS, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 95 | 44% helix, 17% strand | Q00987 |
| B, C, E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 47% helix, 21% strand | Q00987 |
| D | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 46% helix, 15% strand | Q00987 |
| F | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 81 | 46% helix, 10% strand | Q00987 |
Ligands and binding sites
- 6SS · (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl) methyl]-5'-methyl-spiro[1~{h}-indole-3,2'-pyrrolidine]-2-one · ligand · 6 copies · chains A, C, B, D, E, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, E
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.78 | 0.81 | 77 | empty |
| 2 | 901 | 0.74 | 0.78 | 85 | 6SS |
| 3 | 461 | 0.68 | 0.79 | 30 | GOL, 6SS |
| 4 | 178 | 0.58 | 0.82 | 21 | empty |
| 5 | 142 | 0.49 | 0.77 | 19 | 6SS |
Interfaces
9 interfaces between chains.
- C–D · 459 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 421 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 382 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 361 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LAY · Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active… · 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 5LAY · PDBe 5LAY · UniProt Q00987
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