Research workbench
The structure of P38BETA C119S, C162S in complex with a dihydroquinazolinone inhibitor
Analyse The structure of P38BETA C119S, 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
- 3GC9
- Type
- protein
- Length
- 674 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, ZN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 11 (EC 2.7.11.24) | protein | 335 | 39% helix, 15% strand | Q15759 |
| B | Mitogen-activated protein kinase 11 (EC 2.7.11.24) | protein | 339 | 41% helix, 14% 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
- ZN · Zinc ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.72 | 0.80 | 42 | B45 |
| 2 | 507 | 0.71 | 0.80 | 45 | B45 |
| 3 | 404 | 0.64 | 0.78 | 53 | empty |
| 4 | 97 | 0.39 | 0.76 | 15 | empty |
| 5 | 89 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 392 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3GC9 · The structure of p38beta C119S, C162S in complex with a dihydroquinazoli inhibitor · 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 0.97
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 3GC9 · PDBe 3GC9 · UniProt Q15759
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