6DCG: Mitogen-activated protein kinase 1

Discovery of MK-8353: An Orally Bioavailable Dual Mechanism ERK Inhibitor for Oncology. Determined by X-ray diffraction at 1.45 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 3,001
Mol. weight: 43.25 kDa
Ligands: G67
Released: 8 Aug 2018

Explore 6DCG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DCG contains 23 α-helices and 13 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	49-54	6	1
α-helix	60-75	16
β-strand	81	1	2
β-strand	86-88	3	1
β-strand	99-104	6	1
β-strand	108-109	2	2
α-helix	110-116	7
α-helix	118-120	3
α-helix	121-140	20
β-strand	143-144	2	3
α-helix	150-152	3
β-strand	153-155	3	2
β-strand	161-163	3	2
β-strand	170-171	2	3
α-helix	174-176	3
β-strand	178	1	4
α-helix	189-191	3
α-helix	194-197	4
β-strand	200	1	4
α-helix	206-221	16
α-helix	231-242	12
α-helix	245-246	2
α-helix	247-251	5
α-helix	256-264	9
α-helix	266-267	2
α-helix	269-272	4
α-helix	273-276	4
α-helix	282-291	10
α-helix	300-301	2
α-helix	302-306	5
α-helix	309-311	3
α-helix	317-319	3
α-helix	338-349	12
α-helix	350-352	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 1	A	protein	366	Rattus norvegicus	P63086 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DCG_1 Mitogen-activated protein kinase 1 (chains A)
MAHHHHHHMAAAAAAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIK
KISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYK
LLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVA
DPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYL
DQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKML
TFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARF
QPGYRS

Ligands and cofactors

ID	Name	Formula	Copies
G67	(3S)-3-(methylsulfanyl)-1-(2-{4-[4-(1-methyl-1H-1,2,4-triazol-3-yl)phenyl]-3,6-…	C37 H41 N9 O3 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

MK-8353: Discovery of an Orally Bioavailable Dual Mechanism ERK Inhibitor for Oncology. Boga, S.B., Deng, Y., Zhu, L. et al. ACS Med Chem Lett (2018) 9:761-767. DOI 10.1021/acsmedchemlett.8b00220 · PubMed

Other PDB entries of the same protein (UniProt P63086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4S32 1.34 Å, Crystal structure of ERK2 AMP-PNP complex
4S31 1.45 Å, Crystal structure of mitogen-activated protein kinase 1 wtERK2 at 1.45A
5HD4 1.45 Å, Dissecting Therapeutic Resistance to ERK Inhibition Rat Wild Type SCH772984 in complex…
3QYZ 1.46 Å, Crystal structure of ERK2 in complex with an inhibitor
4XP0 1.46 Å, Crystal structure of ERK2 in complex with an inhibitor
4S2Z 1.48 Å, ERK2 Intrinsically active mutant R65S
4S33 1.48 Å, ERK2 R65S mutant complexed with AMP-PNP
6FLE 1.48 Å, Crystal structure of ERK2 in complex with an adenosine derivative
3QYW 1.5 Å, Crystal structure of ERK2 in complex with an inhibitor
8QR7 1.51 Å, Crystal structure of ERK2 in complex with a covalently bound macrocyclic ligand
8QRB 1.51 Å, Crystal structure of ERK2 in complex with a covalently bound macrocyclic ligand
6FI3 1.52 Å, Crystal structure of ERK2 in complex with an adenosine derivative

Browse structure collections

About this viewer

MolViewer shows 6DCG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.