MolNFT v1 · #157963 · protein
Crystal structure of diphosphorylated HPK1 kinase domain in complex with sunitinib in the active state.
6NFZ · Mitogen-activated protein kinase kinase kinase kinase 1: “Crystal structure of diphosphorylated HPK1 kinase domain in complex with sunitinib in the active state.”. X-ray diffraction, 1 ligand (B49), 3 pockets (best druggability…
- 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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