MolNFT v1 · #96879 · protein
Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3- chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3- oxomorpholin-2-YL}ACETIC acid
4JWR · E3 ubiquitin-protein ligase MDM2: “Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3…”. X-ray diffraction, 1 ligand (1MY), 5 pockets (best druggability 0.63). MolNFT v1 #96879 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JWR
- Type
- protein
- Length
- 264 residues
- Chains
- 3
- 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
- 1MY
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 88 | 47% helix, 18% strand | Q00987 |
Ligands and binding sites
- 1MY · {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.63 | 0.81 | 34 | empty |
| 2 | 246 | 0.56 | 0.77 | 25 | 1MY |
| 3 | 114 | 0.47 | 0.78 | 16 | 1MY |
| 4 | 123 | 0.46 | 0.79 | 34 | empty |
| 5 | 104 | 0.45 | 0.78 | 16 | 1MY |
Interfaces
3 interfaces between chains.
- A–B · 593 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JWR · Co-crystal structure of MDM2 with inhibitor {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophen… · 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 4JWR · PDBe 4JWR · UniProt Q00987
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