MolNFT v1 · #129878 · protein
Crystal structure of the ACVR1 (ALK2) kinase in complex with ldn- 212854
5OXG · Activin receptor type-1: “Crystal structure of the ACVR1 (ALK2) kinase in complex with ldn- 212854”. X-ray diffraction, 2 ligands (B4B, CA), 12 pockets (best druggability 0.70). MolNFT v1 #129878 on GenesisL1: 3D structure, binding…
- PDB
- 5OXG
- Type
- protein
- Length
- 1,183 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
- B4B, CA
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-1 (EC 2.7.11.30) | protein | 293 | 39% helix, 21% strand | Q04771 |
| B | Activin receptor type-1 (EC 2.7.11.30) | protein | 296 | 39% helix, 22% strand | Q04771 |
| C | Activin receptor type-1 (EC 2.7.11.30) | protein | 301 | 38% helix, 22% strand | Q04771 |
| D | Activin receptor type-1 (EC 2.7.11.30) | protein | 293 | 39% helix, 21% strand | Q04771 |
Ligands and binding sites
- B4B · 5-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains D
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 | 575 | 0.70 | 0.79 | 67 | B4B |
| 2 | 403 | 0.69 | 0.81 | 45 | B4B |
| 3 | 519 | 0.69 | 0.79 | 60 | empty |
| 4 | 416 | 0.69 | 0.81 | 51 | B4B |
| 5 | 423 | 0.69 | 0.80 | 45 | B4B |
Interfaces
5 interfaces between chains.
- A–C · 620 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 153 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5OXG · Crystal structure of the ACVR1 (ALK2) kinase in complex with LDN-212854 · 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 D against A, TM-score 0.97
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 5OXG · PDBe 5OXG · UniProt Q04771
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