Research workbench
HPK1 in complex with compound 38
Analyse HPK1 in complex with compound 38 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L26
- Type
- protein
- Length
- 1,110 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
- XHM
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 280 | 43% helix, 15% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 275 | 42% helix, 15% strand | Q92918 |
| D | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 275 | 41% helix, 15% strand | Q92918 |
Ligands and binding sites
- XHM · 6-(2-fluoro-6-methylphenyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-5-carbonitrile · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.78 | 0.81 | 90 | XHM |
| 2 | 904 | 0.78 | 0.80 | 92 | XHM |
| 3 | 777 | 0.75 | 0.80 | 70 | XHM |
| 4 | 774 | 0.74 | 0.79 | 59 | empty |
| 5 | 615 | 0.73 | 0.80 | 67 | XHM |
Interfaces
4 interfaces between chains.
- C–D · 2797 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2754 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L26 · HPK1 in complex with compound 38 · 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 7L26 · PDBe 7L26 · UniProt Q92918
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