MolNFT v1 · #107537 · protein
Structure of the stapled peptide ys-02 bound to MDM2
4UD7: “Structure of the stapled peptide ys-02 bound to MDM2”. X-ray diffraction, 3 ligands (2JN, ACE, NH2), 2 pockets (best druggability 0.44). MolNFT v1 #107537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UD7
- Type
- protein
- Length
- 426 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MDM2; Ys-02
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 2JN, ACE, NH2
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MDM2 (EC 6.3.2.-) | protein | 97 | 45% helix, 14% strand | Q00987 |
| B | MDM2 (EC 6.3.2.-) | protein | 96 | 42% helix, 15% strand | Q00987 |
| C, D | MDM2 (EC 6.3.2.-) | protein | 96 | 43% helix, 17% strand | Q00987 |
| F, G | Ys-02 | protein | 12 | 0% helix, 0% strand | — |
| H | Ys-02 | protein | 9 | 0% helix, 0% strand | — |
| I | Ys-02 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2JN · 2-methyl-D-norleucine · ligand · 8 copies · chains A, F, B, G, C, H, D, I
- ACE · Acetyl group · ligand · 2 copies · chains F, H
- NH2 · Amino group · ion · 2 copies · chains A, F, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.44 | 0.77 | 30 | empty |
| 2 | 57 | 0.42 | 0.82 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1101 Ų buried · 23 hydrogen bonds · protein-protein
- A–F · 708 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 699 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 585 Ų buried · 5 hydrogen bonds · protein-protein
- D–I · 479 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 covalent (covalent ligand).
Compared structures
- 4UD7 · Structure of the stapled peptide YS-02 bound to MDM2 · 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 4UD7 · PDBe 4UD7 · UniProt Q00987
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