Research workbench
Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site
Analyse Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YZ4
- Type
- protein
- Length
- 290 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity mitogen-activated protein kinase kinase 7
- EC
- 2.7.12.2
- UniProt
- O14733
- Ligands
- 1E8
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity mitogen-activated protein kinase kinase 7 (EC 2.7.12.2) | protein | 290 | 42% helix, 18% strand | O14733 |
Ligands and binding sites
- 1E8 · 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one · ligand · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.65 | 0.78 | 52 | EDO |
| 2 | 164 | 0.59 | 0.82 | 22 | DMS, 1E8 |
| 3 | 57 | 0.28 | 0.74 | 13 | empty |
Compared structures
- 6YZ4 · Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site · the same entry in another collection · chain A against A, TM-score 1.00
- O14733 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.85
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 O14733
- Elsewhere: RCSB PDB 6YZ4 · PDBe 6YZ4 · UniProt O14733
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