MolNFT v1 · #121145 · protein
HDM2 in complex with a 3,3-disubstituted piperidine
5HMK · E3 ubiquitin-protein ligase MDM2: “HDM2 in complex with a 3,3-disubstituted piperidine”. X-ray diffraction, 1 ligand (62Q), 1 pocket (best druggability 0.79). MolNFT v1 #121145 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5HMK
- Type
- protein
- Length
- 177 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
- 62Q
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 86 | 44% helix, 20% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 91 | 41% helix, 22% strand | Q00987 |
Ligands and binding sites
- 62Q · {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-3-[4-(trifluoromethyl)phenoxy]-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}piperidin-3-yl]methanone · 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 | 966 | 0.79 | 0.80 | 52 | 62Q |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5HMK · 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 5HMK · PDBe 5HMK · UniProt Q00987
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