MolNFT v1 · #145498 · protein
Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology
6CPW · Mitogen-activated protein kinase 1: “Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology”. X-ray diffraction, 2 ligands (F8V, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #145498 on GenesisL1: 3D structure…
- PDB
- 6CPW
- Type
- protein
- Length
- 328 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
- P63086
- Ligands
- F8V, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 328 | 42% helix, 14% strand | P63086 |
Ligands and binding sites
- F8V · (3S)-N-[3-(4-fluorophenyl)-1H-indazol-5-yl]-3-(methylsulfanyl)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl) phenyl]piperazin-1-yl}ethyl)pyrrolidine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.70 | 0.80 | 39 | F8V |
| 2 | 126 | 0.50 | 0.80 | 29 | empty |
| 3 | 88 | 0.37 | 0.76 | 19 | empty |
| 4 | 65 | 0.36 | 0.77 | 12 | empty |
Compared structures
- 6CPW · Discovery of 3(S)-thiomethyl pyrrolidine ERK inhibitors for oncology · the same entry in another collection · chain A against A, TM-score 1.00
- P63086 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 1 (P63086) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P63086
- Elsewhere: RCSB PDB 6CPW · PDBe 6CPW · UniProt P63086
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