MolNFT v1 · #22411 · protein
Structure of human MDM2 in complex with a benzodiazepine inhibitor
1T4E · Ubiquitin-protein ligase E3 MDM2: “Structure of human MDM2 in complex with a benzodiazepine inhibitor”. X-ray diffraction, 1 ligand (DIZ), 4 pockets (best druggability 0.47). MolNFT v1 #22411 on GenesisL1: 3D structure, binding…
- PDB
- 1T4E
- Type
- protein
- Length
- 192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-protein ligase E3 MDM2
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- DIZ
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-protein ligase E3 MDM2 (EC 6.3.2.-) | protein | 96 | 44% helix, 17% strand | Q00987 |
Ligands and binding sites
- DIZ · (4-chlorophenyl)[3-(4-chlorophenyl)-7-iodo-2,5-dioxo-1,2,3,5-tetrahydro-4H-1,4-benzodiazepin-4-yl]acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.47 | 0.77 | 20 | DIZ |
| 2 | 118 | 0.46 | 0.78 | 19 | DIZ |
| 3 | 77 | 0.35 | 0.76 | 19 | empty |
| 4 | 57 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1T4E · Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor · 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 1T4E · PDBe 1T4E · UniProt Q00987
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.