MolNFT v1 · #121142 · protein
HDM2 in complex with a 3,3-disubstituted piperidine
5HMH · E3 ubiquitin-protein ligase MDM2: “HDM2 in complex with a 3,3-disubstituted piperidine”. X-ray diffraction, 2 ligands (62R, SO4), 1 pocket (best druggability 0.79). MolNFT v1 #121142 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HMH
- Type
- protein
- Length
- 194 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
- 62R, SO4
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 95 | 42% helix, 17% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 99 | 38% helix, 17% strand | Q00987 |
Ligands and binding sites
- 62R · 4-[2-(4-{[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]carbonyl}piperazin-1-yl)phenoxy]butanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 970 | 0.79 | 0.80 | 52 | 62R |
Interfaces
1 interface between chains.
- A–B · 499 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5HMH · HDM2 in complex with a 3,3-Disubstituted Piperidine · 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 5HMH · PDBe 5HMH · UniProt Q00987
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