MolNFT v1 · #186311 · protein
Crystal structure of HPK1 in complex with compound 17
7R9T · Hematopoietic progenitor kinase: “Crystal structure of HPK1 in complex with compound 17”. X-ray diffraction, 1 ligand (2TR), 5 pockets (best druggability 0.75). MolNFT v1 #186311 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7R9T
- Type
- protein
- Length
- 576 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
- 2TR
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hematopoietic progenitor kinase (EC 2.7.11.1) | protein | 291 | 45% helix, 15% strand | Q92918 |
| B | Hematopoietic progenitor kinase (EC 2.7.11.1) | protein | 285 | 45% helix, 15% strand | Q92918 |
Ligands and binding sites
- 2TR · 6-amino-3-[(1S,3R)-4'-chloro-3-hydroxy-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridin]-5'-yl]-2-fluoro-N,N-dimethylbenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.75 | 0.80 | 86 | empty |
| 2 | 208 | 0.74 | 0.89 | 32 | 2TR |
| 3 | 175 | 0.72 | 0.89 | 24 | 2TR |
| 4 | 280 | 0.50 | 0.74 | 35 | empty |
| 5 | 89 | 0.39 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2070 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7R9T · Crystal structure of HPK1 in complex with compound 17 · 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 7R9T · PDBe 7R9T · UniProt Q92918
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