MolNFT v1 · #180514 · protein
HPK1 in complex with compound 18
7L25 · Mitogen-activated protein kinase kinase kinase kinase 1: “HPK1 in complex with compound 18”. X-ray diffraction, 1 ligand (XHS), 6 pockets (best druggability 0.79). MolNFT v1 #180514 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7L25
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- 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
- XHS
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 288 | 41% helix, 16% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 288 | 43% helix, 17% strand | Q92918 |
Ligands and binding sites
- XHS · 6-(2-fluoro-6-methoxyphenyl)-1-[6-(4-methylpiperazin-1-yl)pyridin-2-yl]-1H-pyrazolo[4,3-c]pyridine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.79 | 0.85 | 90 | EDO, XHS |
| 2 | 415 | 0.77 | 0.86 | 47 | XHS, EDO |
| 3 | 298 | 0.63 | 0.80 | 41 | EDO |
| 4 | 52 | 0.50 | 0.87 | 18 | empty |
| 5 | 54 | 0.48 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 855 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7L25 · HPK1 in complex with compound 18 · 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 7L25 · PDBe 7L25 · UniProt Q92918
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