MolNFT v1 · #146602 · protein
A multiconformer ligand model of EK6 bound to ERK2
6DMG · Mitogen-activated protein kinase 1: “A multiconformer ligand model of EK6 bound to ERK2”. X-ray diffraction, 2 ligands (EK6, SO4), 3 pockets (best druggability 0.64). MolNFT v1 #146602 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DMG
- Type
- protein
- Length
- 347 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
- EK6, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 347 | 39% helix, 14% strand | P28482 |
Ligands and binding sites
- EK6 · ethyl N-{2-chloro-4-[5-(5-{[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]carbamoyl}-1H-pyrrol-3-yl)-1H-pyrazol-4-yl]benzyl}glycinate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.64 | 0.80 | 35 | EK6 |
| 2 | 135 | 0.55 | 0.82 | 27 | empty |
| 3 | 125 | 0.41 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6DMG · A multiconformer ligand model of EK6 bound to ERK2 · 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 6DMG · PDBe 6DMG · UniProt P28482
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