MolNFT v1 · #41047 · protein
Protein kinase MK2 in complex with an inhibitor (crystal form-2, co- crystallization)
2JBP · MAP kinase-activated protein kinase 2: “Protein kinase MK2 in complex with an inhibitor (crystal form-2, co- crystallization)”. X-ray diffraction, 1 ligand (P4O), 20 pockets (best druggability 0.86). MolNFT v1 #41047 on GenesisL1…
- PDB
- 2JBP
- Type
- protein
- Length
- 3,325 residues
- Chains
- 12
- 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
- P4O
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 12 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 283 | 35% helix, 22% strand | P49137 |
| B | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 290 | 34% helix, 21% strand | P49137 |
| C | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 284 | 35% helix, 20% strand | P49137 |
| D | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 286 | 35% helix, 18% strand | P49137 |
| E | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 282 | 27% helix, 20% strand | P49137 |
| F | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 287 | 36% helix, 22% strand | P49137 |
| G | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 287 | 37% helix, 21% strand | P49137 |
| H | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 282 | 34% helix, 22% strand | P49137 |
| I | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 289 | 36% helix, 19% strand | P49137 |
| J | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 224 | 28% helix, 21% strand | P49137 |
| K | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 264 | 34% helix, 19% strand | P49137 |
| L | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 267 | 22% helix, 19% strand | P49137 |
Ligands and binding sites
- P4O · 2-(2-quinolin-3-ylpyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one · ligand · 11 copies · chains A, B, C, D, E, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.86 | 0.88 | 80 | empty |
| 2 | 729 | 0.84 | 0.88 | 71 | empty |
| 3 | 879 | 0.84 | 0.86 | 96 | empty |
| 4 | 722 | 0.69 | 0.76 | 67 | empty |
| 5 | 714 | 0.69 | 0.76 | 70 | empty |
Interfaces
30 interfaces between chains.
- B–C · 1094 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1083 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1055 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1008 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 999 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2JBP · Protein kinase MK2 in complex with an inhibitor (crystal form-2, co- crystallization) · 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 2JBP · PDBe 2JBP · UniProt P49137
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