MolNFT v1 · #164491 · protein
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009
6SZM · Activin receptor type I: “Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009”. X-ray diffraction, 3 ligands (M2Z, SO4, NH4), 7 pockets (best druggability 0.71). MolNFT v1 #164491 on GenesisL1: 3D…
- 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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