Research workbench
Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 8 (CS275)
Analyse Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T6F
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type 1D
- EC
- 2.7.11.17
- UniProt
- Q8IU85
- Ligands
- MMW
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent protein kinase type 1D (EC 2.7.11.17) | protein | 288 | 38% helix, 16% strand | Q8IU85 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type 1D (EC 2.7.11.17) | protein | 286 | 38% helix, 16% strand | Q8IU85 |
Ligands and binding sites
- MMW · 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.73 | 0.76 | 110 | MMW |
| 2 | 433 | 0.64 | 0.77 | 53 | MMW |
| 3 | 454 | 0.60 | 0.75 | 44 | empty |
| 4 | 62 | 0.38 | 0.79 | 14 | empty |
| 5 | 54 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6T6F · Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IU85 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type 1D… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q8IU85
- Elsewhere: RCSB PDB 6T6F · PDBe 6T6F · UniProt Q8IU85
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