MolNFT v1 · #161290 · protein
Hdmx (14-111; C17S) complexed with compound 14 at 2.4A: structural states of HDM2 and hdmx: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
6Q9S · Protein MDM4: “Hdmx (14-111; C17S) complexed with compound 14 at 2.4A: structural states of HDM2 and hdmx: X-ray elucidation…”. X-ray diffraction, 4 ligands (O4B, HRN, NA), 5 pockets (best druggability 0.59). MolNFT v1 #161290 on…
- PDB
- 6Q9S
- Type
- protein
- Length
- 261 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein MDM4
- UniProt
- O15151
- Ligands
- O4B, HRN, NA, SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein MDM4 | protein | 87 | 45% helix, 20% strand | O15151 |
| C | Protein MDM4 | protein | 88 | 44% helix, 16% strand | O15151 |
| B | Protein MDM4 | protein | 86 | 45% helix, 15% strand | O15151 |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 13 copies · chains A, B, C
- HRN · 3-[[6-chloranyl-3-[3-[(1~{S})-1-(2,4-dichlorophenyl) ethyl]-5-phenyl-imidazol-4-yl]-1~{H}-indol-2-yl]carbonylamino]-4-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]benzoic acid · ligand · 3 copies · chains A, C, B
- NA · Sodium ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B
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 | 316 | 0.59 | 0.77 | 32 | NA, O4B, HRN |
| 2 | 279 | 0.57 | 0.77 | 38 | O4B, SO4 |
| 3 | 117 | 0.44 | 0.77 | 20 | HRN |
| 4 | 107 | 0.42 | 0.76 | 20 | empty |
| 5 | 61 | 0.31 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 460 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 206 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6Q9S · HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 14 AT 2.4A: Structural states of Hdm2 and… · the same entry in another collection · chain A against A, TM-score 1.00
- O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O15151
- Elsewhere: RCSB PDB 6Q9S · PDBe 6Q9S · UniProt O15151
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