MolNFT v1 · #77021 · protein
MK2 kinase bound to compound 5B
3R2B · MAP kinase-activated protein kinase 2: “MK2 kinase bound to compound 5B”. X-ray diffraction, 1 ligand (05B), 20 pockets (best druggability 0.75). MolNFT v1 #77021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3R2B
- Type
- protein
- Length
- 3,264 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
- 05B
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | MAP kinase-activated protein kinase 2 (EC 2.7.11.1) | protein | 272 | 34% helix, 20% strand | P49137 |
Ligands and binding sites
- 05B · 2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one · ligand · 2 copies · chains A, B
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 | 772 | 0.75 | 0.80 | 70 | empty |
| 2 | 565 | 0.74 | 0.82 | 58 | empty |
| 3 | 781 | 0.74 | 0.79 | 90 | empty |
| 4 | 260 | 0.69 | 0.84 | 29 | empty |
| 5 | 371 | 0.67 | 0.81 | 45 | empty |
Interfaces
21 interfaces between chains.
- A–D · 1018 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 1007 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 999 Ų buried · 9 hydrogen bonds · protein-protein
- B–L · 996 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3R2B · MK2 kinase bound to Compound 5b · 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 3R2B · PDBe 3R2B · UniProt P49137
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