MolNFT v1 · #173556 · protein
MEK1 in complex with compound 6
7B3M · Dual specificity mitogen-activated protein kinase kinase 1…: “MEK1 in complex with compound 6”. X-ray diffraction, 4 ligands (ANP, SU5, MG), 9 pockets (best druggability 0.81). MolNFT v1 #173556 on GenesisL1: 3D structure, binding…
- PDB
- 7B3M
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity mitogen-activated protein kinase kinase 1, dual specificity…
- EC
- 2.7.12.2
- UniProt
- Q02750
- Ligands
- ANP, SU5, MG, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity mitogen-activated protein kinase kinase 1, dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 302 | 45% helix, 16% strand | Q02750 |
| B | Dual specificity mitogen-activated protein kinase kinase 1, dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) | protein | 299 | 45% helix, 16% strand | Q02750 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SU5 · 1~{H}-indol-2-yl(pyridin-3-yl)methanone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.81 | 0.83 | 104 | MG, ANP, SU5 |
| 2 | 548 | 0.77 | 0.84 | 69 | MG, ANP, SU5 |
| 3 | 222 | 0.57 | 0.79 | 25 | empty |
| 4 | 219 | 0.56 | 0.79 | 22 | empty |
| 5 | 173 | 0.51 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7B3M · MEK1 in complex with compound 6 · 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 Q02750
- Elsewhere: RCSB PDB 7B3M · PDBe 7B3M · UniProt Q02750
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