Research workbench
Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor
Analyse Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PW4
- Type
- protein
- Length
- 2,630 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE- protein kinase…
- EC
- 2.7.11.1
- UniProt
- Q96Q15, Q8ND04, Q9H0W8
- Ligands
- IHP, 88C, ATP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE- protein kinase SMG1,SERINE/THREONINE-protein kinase SMG1, SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE-protein kinase SMG1,SERINE/THREONINE-protein kinase SMG1 (EC 2.7.11.1) | protein | 1944 | 65% helix, 2% strand | Q96Q15 |
| B | Protein SMG8 | protein | 376 | 51% helix, 11% strand | Q8ND04 |
| C | Protein SMG9 | protein | 310 | 38% helix, 15% strand | Q9H0W8 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
- 88C · 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl) phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.84 | 0.85 | 103 | empty |
| 2 | 1193 | 0.83 | 0.84 | 97 | empty |
| 3 | 1153 | 0.81 | 0.82 | 100 | empty |
| 4 | 407 | 0.80 | 0.88 | 54 | ATP, MG |
| 5 | 1044 | 0.78 | 0.80 | 115 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2425 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 2057 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1017 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7PW5 · Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C- terminus, bound to a SMG1… · a predicted model of the same protein · chain C against C, TM-score 1.00
- 7PW5 · Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1… · a predicted model of the same protein · chain C against C, TM-score 1.00
- 7PW4 · Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
- Q9H0W8 · AlphaFold monomer V2.0 prediction for protein SMG9 (Q9H0W8) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q8ND04 · AlphaFold monomer V2.0 prediction for protein SMG8 (Q8ND04) · a predicted model of the same protein · chain B 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 Q96Q15
- Every structure of UniProt Q8ND04
- Every structure of UniProt Q9H0W8
- Elsewhere: RCSB PDB 7PW4 · PDBe 7PW4 · UniProt Q96Q15 · UniProt Q8ND04 · UniProt Q9H0W8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.