Research workbench
Ordering of the N terminus of human MDM2 by small molecule inhibitors
Analyse Ordering of the N terminus of human MDM2 by small molecule inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HBM
- Type
- protein
- Length
- 814 residues
- Chains
- 8
- 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
- 0Y7
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 106 | 42% helix, 21% strand | Q00987 |
| B, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 104 | 40% helix, 21% strand | Q00987 |
| D | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 99 | 42% helix, 15% strand | Q00987 |
| E, F | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 101 | 41% helix, 15% strand | Q00987 |
| G | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 100 | 42% helix, 14% strand | Q00987 |
| H | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 99 | 41% helix, 14% strand | Q00987 |
Ligands and binding sites
- 0Y7 · {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.79 | 0.81 | 109 | empty |
| 2 | 361 | 0.79 | 0.88 | 32 | 0Y7 |
| 3 | 397 | 0.76 | 0.85 | 34 | 0Y7 |
| 4 | 201 | 0.56 | 0.79 | 25 | 0Y7 |
| 5 | 159 | 0.56 | 0.80 | 22 | 0Y7 |
Interfaces
11 interfaces between chains.
- A–B · 599 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 486 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 478 Ų buried · 0 hydrogen bonds · protein-protein
- A–G · 477 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 408 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4HBM · Ordering of the N Terminus of Human MDM2 by Small Molecule Inhibitors · 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 4HBM · PDBe 4HBM · UniProt Q00987
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