MolNFT v1 · #170350 · protein
Structure of a stapled peptide bound to MDM2
6Y4Q · E3 ubiquitin-protein ligase MDM2: “Structure of a stapled peptide bound to MDM2”. X-ray diffraction, 2 ligands (ACE, O9E), 2 pockets (best druggability 0.42). MolNFT v1 #170350 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6Y4Q
- Type
- protein
- Length
- 208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; ACE-leu-thr-phe-gly-glu-tyr-TRP-ala-gln-leu-ala-ser
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- ACE, O9E
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 92 | 45% helix, 14% strand | Q00987 |
| C, D | ACE-leu-thr-phe-gly-glu-tyr-TRP-ala-gln-leu-ala-ser | protein | 12 | 75% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- O9E · ~{N}-[(1-ethyl-1,2,3-triazol-4-yl)methyl]-~{N},5-dimethyl-4-[2-[2-methyl-5-[methyl-[(1-propyl-1,2,3-triazol-4-yl)methyl]carbamoyl]thiophen-3-yl]cyclopenten-1-yl]thiophene-2-carboxamide · ligand · 2 copies · chains A, C, B, D
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 | 118 | 0.42 | 0.76 | 28 | empty |
| 2 | 60 | 0.33 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 626 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6Y4Q · Structure of a stapled peptide 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 6Y4Q · PDBe 6Y4Q · UniProt Q00987
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