Research workbench
Crystal structure of nonphosphorylated, HPK1 kinase domain in complex with sunitinib in the inactive state.
Analyse Crystal structure of nonphosphorylated, 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
- 6NFY
- Type
- protein
- Length
- 567 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
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 282 | 40% helix, 18% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 285 | 36% helix, 20% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.81 | 0.90 | 43 | empty |
| 2 | 317 | 0.65 | 0.81 | 43 | B49 |
| 3 | 319 | 0.65 | 0.81 | 38 | empty |
| 4 | 253 | 0.61 | 0.80 | 32 | B49 |
| 5 | 228 | 0.53 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2331 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6NFY · Crystal structure of nonphosphorylated, HPK1 kinase domain in complex with sunitinib in… · 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 0.92
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 6NFY · PDBe 6NFY · UniProt Q92918
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