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Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor TL10-105
Analyse Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YG6
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- 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
- OQ8
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity mitogen-activated protein kinase kinase 7 (EC 2.7.12.2) | protein | 284 | 41% helix, 19% strand | O14733 |
| B | Dual specificity mitogen-activated protein kinase kinase 7 (EC 2.7.12.2) | protein | 281 | 41% helix, 18% strand | O14733 |
Ligands and binding sites
- OQ8 · ~{N}-[4-[(4-ethylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]-4-methyl-3-[2-[[(3~{S})-1-propanoylpyrrolidin-3-yl]amino]pyrimidin-4-yl]oxy-benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.75 | 0.85 | 44 | OQ8 |
| 2 | 400 | 0.74 | 0.84 | 45 | OQ8 |
| 3 | 265 | 0.50 | 0.74 | 31 | empty |
| 4 | 83 | 0.35 | 0.75 | 15 | empty |
| 5 | 70 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 6YG6 · Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor TL10-105 · 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 0.96
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 6YG6 · PDBe 6YG6 · UniProt O14733
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