Research workbench
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2
Analyse Fragment-based discovery of a highly potent, orally bioavailable inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GDM
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1
- EC
- 2.7.11.24
- UniProt
- P28482
- Ligands
- F3Z, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 345 | 40% helix, 16% strand | P28482 |
Ligands and binding sites
- F3Z · (3~{R})-1-[2-oxidanylidene-2-[4-(4-pyrimidin-2-ylphenyl)piperazin-1-yl]ethyl]-~{N}-(3-pyridin-4-yl-1~{H}-indazol-5-yl)pyrrolidine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.68 | 0.81 | 41 | F3Z |
| 2 | 130 | 0.57 | 0.83 | 28 | empty |
| 3 | 157 | 0.54 | 0.80 | 21 | empty |
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 6GDM · Fragment-based discovery of a highly potent, orally bioavailable inhibitor which… · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 6GDM · PDBe 6GDM · UniProt P28482
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