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Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009
Analyse Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZM
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activin receptor type I
- EC
- 2.7.11.30
- UniProt
- Q04771
- Ligands
- M2Z, SO4, NH4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type I (EC 2.7.11.30) | protein | 288 | 39% helix, 21% strand | Q04771 |
| B | Activin receptor type I (EC 2.7.11.30) | protein | 295 | 37% helix, 23% strand | Q04771 |
Ligands and binding sites
- M2Z · 1-[4-[4-methyl-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl]piperazine · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.71 | 0.80 | 49 | M2Z |
| 2 | 395 | 0.71 | 0.83 | 38 | M2Z |
| 3 | 413 | 0.67 | 0.79 | 56 | empty |
| 4 | 78 | 0.56 | 0.86 | 18 | empty |
| 5 | 97 | 0.43 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 413 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SZM · Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009 · the same entry in another collection · chain A against A, TM-score 1.00
- Q04771 · AlphaFold monomer V2.0 prediction for activin receptor type-1 (Q04771) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q04771
- Elsewhere: RCSB PDB 6SZM · PDBe 6SZM · UniProt Q04771
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