Research workbench
Crystal structure of MAPKAPK2 (MK2) complexed with pf-3644022 and 5- (4-bromophenyl)-N-[4-(1-PIPERAZINYL)PHENYL]-N-(2-pyridinylmethyl)-2- furancarboxamide
Analyse Crystal structure of MAPKAPK2 (MK2) complexed with pf-3644022 and 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T8X
- Type
- protein
- Length
- 1,664 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAP kinase-activated protein kinase 2
- EC
- 2.7.11.1
- UniProt
- P49137
- Ligands
- B97, MW8, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 279 | 39% helix, 20% strand | P49137 |
| B | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 276 | 38% helix, 21% strand | P49137 |
| C | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 276 | 38% helix, 21% strand | P49137 |
| D | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 280 | 38% helix, 20% strand | P49137 |
| E | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 277 | 38% helix, 21% strand | P49137 |
| F | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 276 | 38% helix, 20% strand | P49137 |
Ligands and binding sites
- B97 · (10R)-10-methyl-3-(6-methylpyridin-3-yl)-9,10,11,12-tetrahydro-8H-[1,4]diazepino[5',6':4,5]thieno[3,2-f]quinolin-8-one · ligand · 6 copies · chains A, B, C, D, E, F
- MW8 · 5-(4-bromophenyl)-~{N}-(4-piperazin-1-ylphenyl)-~{N}-(pyridin-2-ylmethyl)furan-2-carboxamide · ligand · 6 copies · chains A, D, B, C, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.77 | 0.92 | 27 | empty |
| 2 | 214 | 0.71 | 0.87 | 24 | empty |
| 3 | 216 | 0.68 | 0.86 | 24 | empty |
| 4 | 270 | 0.67 | 0.83 | 29 | empty |
| 5 | 689 | 0.67 | 0.75 | 68 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1354 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1282 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1173 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1146 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 633 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6T8X · Crystal structure of MAPKAPK2 (MK2) complexed with PF-3644022 and… · 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 P49137
- Elsewhere: RCSB PDB 6T8X · PDBe 6T8X · UniProt P49137
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