Research workbench
Crystal structure of the ACVR1 kinase domain in complex with ldn- 193189
Analyse Crystal structure of the ACVR1 kinase domain in complex with ldn- 193189 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q4U
- Type
- protein
- Length
- 1,193 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
- LDN
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activin receptor type-1 (EC 2.7.11.30) | protein | 298 | 39% helix, 22% strand | Q04771 |
| B | Activin receptor type-1 (EC 2.7.11.30) | protein | 300 | 38% helix, 23% strand | Q04771 |
| C | Activin receptor type-1 (EC 2.7.11.30) | protein | 296 | 39% helix, 22% strand | Q04771 |
| D | Activin receptor type-1 (EC 2.7.11.30) | protein | 299 | 40% helix, 22% strand | Q04771 |
Ligands and binding sites
- LDN · 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, C, B, D
- FLC · Citrate anion · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.87 | 0.88 | 127 | EDO, LDN |
| 2 | 330 | 0.74 | 0.86 | 36 | LDN |
| 3 | 239 | 0.74 | 0.88 | 32 | LDN |
| 4 | 554 | 0.74 | 0.81 | 64 | empty |
| 5 | 505 | 0.72 | 0.81 | 51 | LDN, EDO |
Interfaces
5 interfaces between chains.
- A–B · 1153 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 424 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 284 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3Q4U · Crystal structure of the ACVR1 kinase domain in complex with LDN-193189 · 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 C 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 3Q4U · PDBe 3Q4U · UniProt Q04771
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