Research workbench
Crystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36.
Analyse Crystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OY6
- Type
- protein
- Length
- 1,166 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activin receptor type-1
- EC
- 2.7.11.30
- UniProt
- Q04771
- Ligands
- B4E
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Activin receptor type-1 (EC 2.7.11.30) | protein | 291 | 38% helix, 22% strand | Q04771 |
| B | Activin receptor type-1 (EC 2.7.11.30) | protein | 292 | 40% helix, 22% strand | Q04771 |
| D | Activin receptor type-1 (EC 2.7.11.30) | protein | 292 | 39% helix, 22% strand | Q04771 |
Ligands and binding sites
- B4E · cyclical inhibitor OD36 · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.76 | 0.80 | 69 | empty |
| 2 | 804 | 0.73 | 0.78 | 85 | B4E |
| 3 | 460 | 0.72 | 0.82 | 50 | B4E, EDO |
| 4 | 447 | 0.71 | 0.82 | 53 | B4E |
| 5 | 392 | 0.70 | 0.82 | 49 | B4E |
Interfaces
6 interfaces between chains.
- A–C · 385 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 306 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5OY6 · Crystal structure of the ACVR1 (ALK2) kinase in complex with cyclical inhibitor OD36. · the same entry in another collection · chain D against D, 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 0.96
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 5OY6 · PDBe 5OY6 · UniProt Q04771
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