9LTA: Compound SKLB-D18 with MAPK7

Crystal Structure of Compound SKLB-D18 with MAPK7 (ERK5). Determined by X-ray diffraction at 2.33 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,482
Mol. weight: 80.43 kDa
Ligands: A1EKR
Released: 2 Apr 2025

Explore 9LTA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LTA contains 45 α-helices and 20 β-strands across 2 chains. 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: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	55-62	8	3
β-strand	68-74	7	3
β-strand	80-86	7	3
α-helix	93-108	16
β-strand	114	1	4
β-strand	117-120	4	3
β-strand	133-137	5	3
β-strand	142-143	2	4
α-helix	144-148	5
α-helix	156-175	20
β-strand	179	1	5
α-helix	185-187	3
β-strand	188-190	3	4
β-strand	196-198	3	4
β-strand	205	1	5
α-helix	230-233	4
α-helix	242-257	16
α-helix	267-278	12
α-helix	281-282	2
α-helix	283-288	6
α-helix	292-299	8
α-helix	302-303	2
α-helix	305-308	4
α-helix	309-312	4
α-helix	318-327	10
α-helix	332-334	3
α-helix	336-337	2
α-helix	338-342	5
α-helix	345-347	3
α-helix	353-355	3
α-helix	362-364	3
α-helix	366-369	4
α-helix	374-390	17

Chain B: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-62	8	1
β-strand	68-74	7	1
β-strand	80-86	7	1
α-helix	93-108	16
β-strand	114	1	2
β-strand	117-120	4	1
α-helix	127-129	3
β-strand	133-138	6	1
β-strand	142-143	2	2
α-helix	144-148	5
α-helix	156-174	19
α-helix	185-187	3
β-strand	188-190	3	2
β-strand	196-198	3	2
α-helix	213-217	5
α-helix	230-233	4
α-helix	242-257	16
α-helix	267-278	12
α-helix	281-282	2
α-helix	283-288	6
α-helix	292-299	8
α-helix	306-308	3
α-helix	309-312	4
α-helix	318-327	10
α-helix	332-334	3
α-helix	336-337	2
α-helix	338-342	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 7	A, B	protein	346	Homo sapiens	Q13164 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9LTA_1 Mitogen-activated protein kinase 7 (chains A, B)
TFDVGDEYEIIETIGNGAYGVVSSRRRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILK
HFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLL
RGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWY
RAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQ
AVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFL
AKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARRE

Ligands and cofactors

ID	Name	Formula	Copies
A1EKR	4-[5-chloranyl-2-[[3-[(dimethylamino)methyl]phenyl]amino]pyrimidin-4-yl]-~{N}-m…	C22 H25 Cl N6 O2 S	2

Primary citation

A first-in-class selective inhibitor of ERK1/2 and ERK5 overcomes drug resistance with a single-molecule strategy. Xiao, H., Wang, A., Shuai, W. et al. Signal Transduct Target Ther (2025) 10:70-70. DOI 10.1038/s41392-025-02169-z · 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
5O7I 2.38 Å, ERK5 in complex with a pyrrole inhibitor
6HKM 2.47 Å, Crystal structure of Compound 1 with ERK5
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

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