Research workbench
Crystal structure of HDM2 in complex with nutlin-3A
Analyse Crystal structure of HDM2 in complex with nutlin-3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C5A
- Type
- protein
- Length
- 184 residues
- Chains
- 2
- 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
- NUT, IOD, SO4, CL
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 92 | 43% helix, 22% strand | Q00987 |
Ligands and binding sites
- NUT · 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.50 | 0.78 | 27 | IOD |
| 2 | 163 | 0.48 | 0.76 | 23 | NUT, CL |
| 3 | 92 | 0.42 | 0.77 | 17 | NUT |
Interfaces
1 interface between chains.
- A–B · 465 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5C5A · Crystal Structure of HDM2 in complex with Nutlin-3a · 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 5C5A · PDBe 5C5A · UniProt Q00987
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