Research workbench
Phospho-ERK2 bound to bivalent inhibitor SBP3
Analyse Phospho-ERK2 bound to bivalent inhibitor SBP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V62
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1; Ribosomal protein S6 kinase alpha-1
- EC
- 2.7.11.24, 2.7.11.1
- UniProt
- P28482, Q15418
- Ligands
- FRZ, AKS
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 351 | 40% helix, 15% strand | P28482 |
| I | Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1) | protein | 14 | 57% helix, 0% strand | Q15418 |
Ligands and binding sites
- FRZ · 5-(2-phenylpyrazolo[1,5-a]pyridin-3-yl)-1H-pyrazolo[3, 4-c]pyridazin-3-amine · ligand · chains A
- AKS · N-(hex-5-yn-1-yl)hexanamide · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.67 | 0.80 | 38 | FRZ, AKS |
| 2 | 83 | 0.59 | 0.88 | 16 | empty |
| 3 | 70 | 0.33 | 0.76 | 15 | empty |
| 4 | 55 | 0.29 | 0.75 | 15 | empty |
| 5 | 55 | 0.25 | 0.72 | 13 | GOL |
Interfaces
1 interface between chains.
- A–I · 680 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
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 P28482
- Every structure of UniProt Q15418
- Elsewhere: RCSB PDB 5V62 · PDBe 5V62 · UniProt P28482 · UniProt Q15418
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