Research workbench
Structure of a hit for G protein coupled receptor kinase 2 (GRK2) inhibitor for the potential treatment of heart failure
Analyse Structure of a hit for G protein coupled receptor kinase 2 (GRK2) inhibitor for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K7L
- Type
- protein
- Length
- 1,012 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-adrenergic receptor kinase 1; Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
- EC
- 2.7.11.15
- UniProt
- P25098, P62873, P59768
- Ligands
- W4D, MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-adrenergic receptor kinase 1 (EC 2.7.11.15) | protein | 616 | 44% helix, 16% strand | P25098 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 6% helix, 48% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 53% helix, 0% strand | P59768 |
Ligands and binding sites
- W4D · 3-benzyl-6-(1H-pyrazol-4-yl)quinazolin-4(3H)-one · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.77 | 0.84 | 50 | empty |
| 2 | 308 | 0.67 | 0.82 | 34 | W4D |
| 3 | 372 | 0.58 | 0.75 | 39 | empty |
| 4 | 220 | 0.54 | 0.78 | 29 | empty |
| 5 | 54 | 0.47 | 0.85 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–G · 2249 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1131 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7K7L · Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the… · the same entry in another collection · chain A against A, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P25098 · AlphaFold monomer V2.0 prediction for beta-adrenergic receptor kinase 1 (P25098) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.92
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 P25098
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7K7L · PDBe 7K7L · UniProt P25098 · UniProt P62873 · UniProt P59768
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