MolNFT v1 · #124075 · protein
Crystal structure of ERK2 in complex with compound 22
5K4I · Mitogen-activated protein kinase 1: “Crystal structure of ERK2 in complex with compound 22”. X-ray diffraction, 1 ligand (6QB), 3 pockets (best druggability 0.68). MolNFT v1 #124075 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K4I
- Type
- protein
- Length
- 336 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
- 6QB
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 336 | 39% helix, 16% strand | P28482 |
Ligands and binding sites
- 6QB · 1-[(1~{S})-1-(4-chloranyl-3-fluoranyl-phenyl)-2-oxidanyl-ethyl]-4-[2-[(2-methylpyrazol-3-yl) amino]pyrimidin-4-yl]pyridin-2-one · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.68 | 0.81 | 35 | 6QB, EDO |
| 2 | 57 | 0.38 | 0.80 | 18 | empty |
| 3 | 85 | 0.33 | 0.74 | 18 | empty |
Compared structures
- 5K4I · Crystal Structure of ERK2 in complex with compound 22 · 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 5K4I · PDBe 5K4I · UniProt P28482
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