MolNFT v1 · #161283 · protein
HDM2 (17-111, wildtype) complexed with compound 9 at 1.13A; structural states of HDM2 and hdmx: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
6Q9L · E3 ubiquitin-protein ligase MDM2: “HDM2 (17-111, wildtype) complexed with compound 9 at 1.13A; structural states of HDM2 and hdmx: X-ray…”. X-ray diffraction, 2 ligands (HTZ, CL), 3 pockets (best druggability 0.46). MolNFT v1…
- PDB
- 6Q9L
- 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
- HTZ, CL
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 94 | 44% helix, 17% strand | Q00987 |
Ligands and binding sites
- HTZ · [6-chloranyl-3-[3-[[4-chloranyl-2-(hydroxymethyl) phenyl]methyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]-[(3~{S})-3-[3-(dimethylamino)propyl-methyl-amino]pyrrolidin-1-yl]methanone · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 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 | 136 | 0.46 | 0.77 | 21 | HTZ, CL |
| 2 | 131 | 0.46 | 0.77 | 20 | HTZ, CL |
| 3 | 80 | 0.31 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 71 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Q9L · HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and… · 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 6Q9L · PDBe 6Q9L · UniProt Q00987
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