MolNFT v1 · #70137 · protein
Structure of human MDM2 protein in complex with mi-63-analog
3LBL · E3 ubiquitin-protein ligase MDM2: “Structure of human MDM2 protein in complex with mi-63-analog”. X-ray diffraction, 1 ligand (MI6), 4 pockets (best druggability 0.60). MolNFT v1 #70137 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LBL
- Type
- protein
- Length
- 270 residues
- Chains
- 3
- 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
- MI6
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 94 | 44% helix, 18% strand | Q00987 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 91 | 47% helix, 20% strand | Q00987 |
| E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 85 | 49% helix, 18% strand | Q00987 |
Ligands and binding sites
- MI6 · (2'R,3R,4'R,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(2-morpholin-4-ylethyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.60 | 0.77 | 30 | MI6 |
| 2 | 118 | 0.49 | 0.79 | 17 | MI6 |
| 3 | 105 | 0.44 | 0.77 | 16 | MI6 |
| 4 | 89 | 0.34 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–E · 562 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 326 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 196 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3LBL · Structure of human MDM2 protein in complex with Mi-63-analog · 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 3LBL · PDBe 3LBL · UniProt Q00987
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