Research workbench
The structure of P38BETA C162S in complex with a dihydroquinazolinone
Analyse The structure of P38BETA C162S in complex with a dihydroquinazolinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GC8
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 11
- EC
- 2.7.11.24
- UniProt
- Q15759
- Ligands
- B45, NA, NI
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 11 (EC 2.7.11.24) | protein | 347 | 39% helix, 15% strand | Q15759 |
| B | Mitogen-activated protein kinase 11 (EC 2.7.11.24) | protein | 346 | 36% helix, 15% strand | Q15759 |
Ligands and binding sites
- B45 · 5-(2-chloro-4-fluorophenyl)-1-(2,6-dichlorophenyl)-7-[1-(1-methylethyl)piperidin-4-yl]-3,4-dihydroquinazolin-2(1H)-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.79 | 0.83 | 69 | B45 |
| 2 | 712 | 0.76 | 0.81 | 71 | B45 |
| 3 | 466 | 0.66 | 0.78 | 60 | empty |
| 4 | 57 | 0.33 | 0.77 | 14 | empty |
| 5 | 51 | 0.33 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 441 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GC8 · The structure of p38beta C162S in complex with a dihydroquinazoli · the same entry in another collection · chain A against A, TM-score 1.00
- Q15759 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 11 (Q15759) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q15759
- Elsewhere: RCSB PDB 3GC8 · PDBe 3GC8 · UniProt Q15759
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