Research workbench
Phospho-ERK2 bound to bivalent inhibitor SBP2
Analyse Phospho-ERK2 bound to bivalent inhibitor SBP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V61
- Type
- protein
- Length
- 367 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,PROTEIN tat
- EC
- 2.7.11.24, 2.7.11.1
- UniProt
- P28482, Q15418, P04608
- Ligands
- FRZ, 90A
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 350 | 42% helix, 15% strand | P28482 |
| I | Ribosomal protein S6 kinase alpha-1,PROTEIN tat (EC 2.7.11.1) | protein | 17 | 29% helix, 0% strand | Q15418, P04608 |
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
- 90A · 2-oxo-6,9,12,15-tetraoxa-3-azaoctadecan-18-oic acid · ligand · chains A, I
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.68 | 0.84 | 29 | FRZ |
| 2 | 163 | 0.55 | 0.80 | 30 | empty |
| 3 | 159 | 0.50 | 0.78 | 27 | empty |
| 4 | 88 | 0.39 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–I · 795 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, covalent ligand).
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
- Every structure of UniProt P04608
- Elsewhere: RCSB PDB 5V61 · PDBe 5V61 · UniProt P28482 · UniProt Q15418 · UniProt P04608
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