Research workbench
Crystal structure of HPK1 in complex with compound 14
Analyse Crystal structure of HPK1 in complex with compound 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R9P
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hematopoietic progenitor kinase
- EC
- 2.7.11.1
- UniProt
- Q92918
- Ligands
- 2WI, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hematopoietic progenitor kinase (EC 2.7.11.1) | protein | 287 | 44% helix, 15% strand | Q92918 |
| B | Hematopoietic progenitor kinase (EC 2.7.11.1) | protein | 291 | 43% helix, 15% strand | Q92918 |
Ligands and binding sites
- 2WI · 6-amino-2-fluoro-N,N-dimethyl-3-(4'-methylspiro[cyclopropane-1,3'-pyrrolo[2,3-b]pyridin]-5'-yl)benzamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.77 | 0.81 | 71 | empty |
| 2 | 153 | 0.72 | 0.90 | 24 | 2WI |
| 3 | 167 | 0.71 | 0.89 | 25 | 2WI |
| 4 | 115 | 0.46 | 0.78 | 25 | empty |
| 5 | 187 | 0.42 | 0.73 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2054 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7R9P · Crystal structure of HPK1 in complex with compound 14 · 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 7R9P · PDBe 7R9P · UniProt Q92918
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