MolNFT v1 · #181633 · protein
HPK1 in complex with compound 1
7M0M · Mitogen-activated protein kinase kinase kinase kinase 1: “HPK1 in complex with compound 1”. X-ray diffraction, 1 ligand (YK1), 6 pockets (best druggability 0.79). MolNFT v1 #181633 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7M0M
- Type
- protein
- Length
- 584 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
- YK1
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 293 | 41% helix, 16% strand | Q92918 |
| B | Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7.11.1) | protein | 291 | 43% helix, 16% strand | Q92918 |
Ligands and binding sites
- YK1 · 4-[2-fluoro-6-(trifluoromethyl)anilino]-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl) amino]pyrimidine-5-carboxamide · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.79 | 0.80 | 87 | empty |
| 2 | 216 | 0.65 | 0.84 | 30 | YK1 |
| 3 | 235 | 0.65 | 0.83 | 31 | YK1 |
| 4 | 227 | 0.45 | 0.73 | 31 | empty |
| 5 | 51 | 0.30 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1939 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7M0M · HPK1 in complex with compound 1 · 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 7M0M · PDBe 7M0M · UniProt Q92918
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