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HDM2 (17-111, wild type) complexed with compound 12 at 1.8A; structural states of HDM2 and hdmx: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
Analyse HDM2 (17-111, wild type) complexed with compound 12 at 1.8A; structural states… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q96
- Type
- protein
- Length
- 173 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- HRE, SO4
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 87 | 43% helix, 15% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 86 | 45% helix, 15% strand | Q00987 |
Ligands and binding sites
- HRE · 4-[(4~{S})-5-(5-chloranyl-2-oxidanylidene-1~{H}-pyridin-3-yl)-2-[2-(dimethylamino)-4-methoxy-pyrimidin-5-yl]-6-oxidanylidene-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-4-yl]benzenecarbonitrile · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.76 | 0.84 | 34 | HRE |
| 2 | 103 | 0.43 | 0.77 | 19 | HRE |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Q96 · HDM2 (17-111, WILD TYPE) COMPLEXED WITH COMPOUND 12 AT 1.8A; Structural states of Hdm2… · 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 6Q96 · PDBe 6Q96 · UniProt Q00987
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