MolNFT v1 · #161286 · protein
HDM2 (17-111, wildtype) complexed with compound 10 at 1.21A; structural states of HDM2 and hdmx: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
6Q9O · E3 ubiquitin-protein ligase MDM2: “HDM2 (17-111, wildtype) complexed with compound 10 at 1.21A; structural states of HDM2 and hdmx: X-ray…”. X-ray diffraction, 1 ligand (HU8), 1 pocket (best druggability 0.82). MolNFT v1 #161286 on…
- PDB
- 6Q9O
- Type
- protein
- Length
- 188 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
- HU8
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 94 | 45% helix, 21% strand | Q00987 |
Ligands and binding sites
- HU8 · ~{N}-~{tert}-butyl-2-[4-chloranyl-2-[5-(3-chloranyl-4-fluoranyl-phenyl)-2-cyclohexyl-4-(1~{H}-1,2,3,4-tetrazol-5-yl)imidazol-1-yl]phenyl]ethanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.82 | 0.82 | 58 | HU8 |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6Q9O · HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; 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 6Q9O · PDBe 6Q9O · UniProt Q00987
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