Research workbench
Structure of human myotonic dystrophy protein kinase in complex with the bisindoylmaleide inhibitor bim VIII
Analyse Structure of human myotonic dystrophy protein kinase in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VD5
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dmpk protein
- EC
- 2.7.11.1
- UniProt
- Q6P5Z6
- Ligands
- BI8
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dmpk protein (EC 2.7.11.1) | protein | 390 | 42% helix, 14% strand | Q6P5Z6 |
| B | Dmpk protein (EC 2.7.11.1) | protein | 380 | 42% helix, 13% strand | Q6P5Z6 |
Ligands and binding sites
- BI8 · 3-[1-(3-aminopropyl)-1H-indol-3-yl]-4-(1-methyl-1H-indol-3-yl)-1H-pyrrole-2,5-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.74 | 0.77 | 101 | BI8 |
| 2 | 481 | 0.69 | 0.80 | 45 | BI8 |
| 3 | 115 | 0.62 | 0.87 | 20 | empty |
| 4 | 155 | 0.61 | 0.84 | 27 | empty |
| 5 | 93 | 0.37 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 629 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2VD5 · Structure of Human Myotonic Dystrophy Protein Kinase in Complex with the Bisindoylmaleide… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6P5Z6
- Elsewhere: RCSB PDB 2VD5 · PDBe 2VD5 · UniProt Q6P5Z6
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