MolNFT v1 · #151315 · protein
Human RIOK2 bound to inhibitor
6HK6 · SERINE/THREONINE-protein kinase RIO2: “Human RIOK2 bound to inhibitor”. X-ray diffraction, 2 ligands (G8H, CL), 20 pockets (best druggability 0.88). MolNFT v1 #151315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HK6
- Type
- protein
- Length
- 2,869 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase RIO2
- EC
- 2.7.11.1
- UniProt
- Q9BVS4
- Ligands
- G8H, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, J | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 290 | 38% helix, 22% strand | Q9BVS4 |
| E | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 289 | 38% helix, 22% strand | Q9BVS4 |
| F | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 289 | 38% helix, 22% strand | Q9BVS4 |
| G | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 271 | 40% helix, 22% strand | Q9BVS4 |
| H | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 282 | 39% helix, 20% strand | Q9BVS4 |
| I | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 288 | 38% helix, 19% strand | Q9BVS4 |
Ligands and binding sites
- G8H · 2-naphthalen-2-yl-~{N}-pyridin-2-yl-ethanamide · ligand · 10 copies · chains A, F, B, I, C, D, E, G, H, J
- CL · Chloride ion · ion · 4 copies · chains A, H, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, B, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, C, D, E, F, H
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 | 654 | 0.88 | 0.92 | 81 | empty |
| 2 | 772 | 0.87 | 0.91 | 76 | empty |
| 3 | 494 | 0.86 | 0.92 | 76 | EDO |
| 4 | 716 | 0.81 | 0.85 | 66 | empty |
| 5 | 611 | 0.79 | 0.84 | 71 | G8H |
Interfaces
16 interfaces between chains.
- C–F · 2084 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2063 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2020 Ų buried · 28 hydrogen bonds · protein-protein
- G–J · 1572 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 955 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 Q9BVS4
- Elsewhere: RCSB PDB 6HK6 · PDBe 6HK6 · UniProt Q9BVS4
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