Research workbench
Crystal structure of C-terminal domain of MSK1 in complex with covalently bound with literature RSK2 inhibitor indazole cyanoacrylamide compound 26 (soak)
Analyse Crystal structure of C-terminal domain of MSK1 in complex with covalently bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UP7
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6 kinase alpha-5
- EC
- 2.7.11.1
- UniProt
- O75582
- Ligands
- 1LE
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 277 | 44% helix, 17% strand | O75582 |
| B | Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1) | protein | 280 | 45% helix, 17% strand | O75582 |
Ligands and binding sites
- 1LE · (2S)-2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-[3-(3, 4,5-trimethoxyphenyl)-1H-indazol-5-yl]propanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.63 | 0.80 | 32 | 1LE |
| 2 | 287 | 0.60 | 0.79 | 33 | 1LE |
| 3 | 67 | 0.53 | 0.86 | 14 | empty |
| 4 | 56 | 0.50 | 0.86 | 14 | empty |
| 5 | 112 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 299 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7UP7 · Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound with… · the same entry in another collection · chain A against A, TM-score 1.00
- O75582 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-5 (O75582) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O75582
- Elsewhere: RCSB PDB 7UP7 · PDBe 7UP7 · UniProt O75582
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