Research workbench
HPK1 in complex with compound 1
Analyse HPK1 in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M0K
- Type
- protein
- Length
- 1,152 residues
- Chains
- 4
- 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
- YK7
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 289 | 42% helix, 17% strand | Q92918 |
| B, C | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 287 | 44% helix, 16% strand | Q92918 |
Ligands and binding sites
- YK7 · 4-anilino-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.84 | 0.85 | 133 | empty |
| 2 | 1199 | 0.83 | 0.84 | 107 | YK7 |
| 3 | 589 | 0.68 | 0.78 | 43 | empty |
| 4 | 181 | 0.67 | 0.86 | 28 | YK7 |
| 5 | 159 | 0.65 | 0.85 | 21 | YK7 |
Interfaces
4 interfaces between chains.
- C–D · 2436 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2427 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7M0K · HPK1 in complex with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00
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 7M0K · PDBe 7M0K · UniProt Q92918
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