6HKM: Compound 1 with ERK5

Crystal structure of Compound 1 with ERK5. Determined by X-ray diffraction at 2.47 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,711
Mol. weight: 40.19 kDa
Ligands: G92
Released: 27 Feb 2019

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

Secondary structure: helices and β-sheets

6HKM contains 26 α-helices and 11 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: 26 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	59-62	4	1
β-strand	69-71	3	1
β-strand	82-86	5	1
α-helix	93-108	16
β-strand	114	1	2
β-strand	119-120	2	1
α-helix	127-129	3
β-strand	133-137	5	1
β-strand	142-143	2	2
α-helix	144-148	5
α-helix	156-175	20
β-strand	179	1	3
α-helix	185-187	3
β-strand	188-190	3	2
β-strand	196-198	3	2
β-strand	205	1	3
α-helix	214-216	3
α-helix	219-221	3
α-helix	225-227	3
α-helix	230-234	5
α-helix	242-257	16
α-helix	267-278	12
α-helix	281-282	2
α-helix	283-287	5
α-helix	292-300	9
α-helix	306-308	3
α-helix	309-312	4
α-helix	318-325	8
α-helix	332-334	3
α-helix	336-337	2
α-helix	338-341	4
α-helix	345-347	3
α-helix	353-355	3
α-helix	362-364	3
α-helix	366-369	4
α-helix	374-389	16
α-helix	390-394	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 7	A	protein	347	Homo sapiens	Q13164 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HKM_1 Mitogen-activated protein kinase 7 (chains A)
FDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKH
FKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLR
GLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYR
APELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQA
VGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLA
KYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGI

Ligands and cofactors

ID	Name	Formula	Copies
G92	[4-(6,7-dimethoxyquinazolin-4-yl)piperidin-1-yl]-[4-(trifluoromethyloxy)phenyl]…	C23 H22 F3 N3 O4	1

Primary citation

Discovery and Characterization of the Potent and Highly Selective (Piperidin-4-yl)pyrido[3,2- d]pyrimidine Based in Vitro Probe BAY-885 for the Kinase ERK5. Nguyen, D., Lemos, C., Wortmann, L. et al. J Med Chem (2019) 62:928-940. DOI 10.1021/acs.jmedchem.8b01606 · PubMed

Other PDB entries of the same protein (UniProt Q13164 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BYZ 1.65 Å, ERK5 in complex with small molecule
4ZSG 1.79 Å, Mitogen activated protein kinase 7 in complex with inhibitor
2Q8Y 2.0 Å, Structural insight into the enzymatic mechanism of the phophothreonine lyase
4ZSL 2.25 Å, Mitogen activated protein kinase 7 in complex with inhibitor
6HKN 2.33 Å, Crystal structure of Compound 35 with ERK5
9LTA 2.33 Å, Crystal Structure of Compound SKLB-D18 with MAPK7 (ERK5)
5O7I 2.38 Å, ERK5 in complex with a pyrrole inhibitor
4ZSJ 2.48 Å, Mitogen activated protein kinase 7 in complex with inhibitor
7PUS 2.59 Å, ERK5 in complex with Pyrrole Carboxamide scaffold
4IC7 2.6 Å, Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment
5BYY 2.79 Å, ERK5 in complex with small molecule
4B99 2.8 Å, Crystal Structure of MAPK7 (ERK5) with inhibitor

Browse structure collections

About this viewer

MolViewer shows 6HKM 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.