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
- 7M0L
- 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
- YK4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% 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 | 43% helix, 17% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 285 | 42% helix, 16% strand | Q92918 |
| C | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 289 | 42% helix, 16% strand | Q92918 |
Ligands and binding sites
- YK4 · 4-(2-bromoanilino)-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
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.83 | 0.84 | 100 | empty |
| 2 | 1156 | 0.81 | 0.82 | 106 | empty |
| 3 | 587 | 0.74 | 0.81 | 49 | empty |
| 4 | 249 | 0.70 | 0.85 | 39 | YK4 |
| 5 | 652 | 0.67 | 0.76 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2523 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2438 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 208 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7M0L · HPK1 in complex with compound 1 · the same entry in another collection · chain B against B, 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 7M0L · PDBe 7M0L · UniProt Q92918
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