MolNFT v1 · #21414 · protein

X-ray structure of the human mitogen-activated protein kinase kinase 2 (MEK2)IN a complex with ligand and mgatp

1S9I · Dual specificity mitogen-activated protein kinase kinase 2: “X-ray structure of the human mitogen-activated protein kinase kinase 2 (MEK2)IN a complex with ligand and…”. X-ray diffraction, 3 ligands (ATP, 5EA, MG), 7 pockets (best…

PDB: 1S9I
Type: protein
Length: 594 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity mitogen-activated protein kinase kinase 2
EC: 2.7.1.37
UniProt: P36507
Ligands: ATP, 5EA, MG
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.1.37)	protein	303	41% helix, 14% strand	P36507
B	Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.1.37)	protein	291	40% helix, 16% strand	P36507

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
5EA · 5-{3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}-N-(2-morpholin-4-ylethyl)-1,3,4-oxadiazol-2-amine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.80	0.84	77	MG, ATP, 5EA
2	571	0.78	0.84	54	MG, ATP, 5EA
3	225	0.52	0.77	28	empty
4	133	0.47	0.78	23	empty
5	103	0.45	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 765 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1S9I · X-ray structure of the human mitogen-activated protein kinase kinase 2 (MEK2)in a complex… · the same entry in another collection · chain A against A, TM-score 1.00
P36507 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P36507
Elsewhere: RCSB PDB 1S9I · PDBe 1S9I · UniProt P36507

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