Research workbench
Crystal structure of diphosphorylated HPK1 kinase domain in complex with sunitinib in the active state.
Analyse Crystal structure of diphosphorylated HPK1 kinase domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NFZ
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase kinase 1
- EC
- 2.7.11.1
- UniProt
- Q92918
- Ligands
- B49
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 270 | 36% helix, 13% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 277 | 37% helix, 18% strand | Q92918 |
Ligands and binding sites
- B49 · N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide · ligand · 2 copies · chains A, B
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 | 733 | 0.72 | 0.78 | 89 | B49 |
| 2 | 650 | 0.68 | 0.76 | 73 | B49 |
| 3 | 79 | 0.37 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6NFZ · Crystal structure of diphosphorylated HPK1 kinase domain in complex with sunitinib in the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92918 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q92918
- Elsewhere: RCSB PDB 6NFZ · PDBe 6NFZ · UniProt Q92918
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