7W5O

Crystal structure of ERK2 with an allosteric inhibitor

PDB DOI: https://doi.org/10.2210/pdb7W5O/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-11-30 Released: 2022-02-23
Deposition Author(s): Yoshida, M., Kinoshita, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.279
R-Value Work: 0.225
R-Value Observed: 0.228

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Identification of a novel target site for ATP-independent ERK2 inhibitors.

Yoshida, M., Nagao, H., Sugiyama, H., Sawa, M., Kinoshita, T.

(2022) Biochem Biophys Res Commun 593: 73-78

PubMed: 35063772 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2022.01.035
Primary Citation of Related Structures:
7W5O

PubMed Abstract:
Extracellular signal-regulated kinase 2 (ERK2) controls vital physiological processes involving proliferation and differentiation and is a drug target molecule for many diseases such as cancers. In silico screening focusing on an allosteric site that plays a crucial role in substrate anchoring conferred an ERK2 inhibitor (compound 1). However, a competitive binding assay indicated that compound 1 did not bind to the allosteric site. Here, the crystal structure of ERK2 in complex with compound 1 revealed a novel binding site. This finding demonstrates the feasibility of developing new types of ERK2 inhibitors.

Organizational Affiliation

Graduate School of Science, Osaka Prefecture University, Osaka, 599-8531, Japan.

Macromolecule Content

Total Structure Weight: 87 kDa
Atom Count: 5,973
Modelled Residue Count: 696
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A, B	368	Homo sapiens	Mutation(s): 0 Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482 Go to UniProtKB: P28482
PHAROS: P28482 GTEx: ENSG00000100030
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28482
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6GI Query on 6GI Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	13-[4-({Imidazo[1,2-a]pyridin-2-yl}methoxy)phenyl]-4,8-dioxa-12,14,16,18-tetraazatetracyclo[9.7.0.0^{3,9}.0^{12,17}]octadeca-1(11),2,9,15,17-pentaen-15-amine C₂₆ H₂₃ N₇ O₃ YNNIPDFDZWDMRE-XMMPIXPASA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
5ID Query on 5ID Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL C₁₁ H₁₃ I N₄ O₄ WHSIXKUPQCKWBY-IOSLPCCCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	J [auth A], O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A]	E [auth A], G [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] H [auth A] I [auth A] K [auth B] M [auth B] D [auth A], H [auth A], I [auth A], K [auth B], M [auth B], N [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP Query on NEP	A, B	L-PEPTIDE LINKING	C₆ H₁₀ N₃ O₅ P		HIS

Binding Affinity Annotations
ID	Source	Binding Affinity
5ID	BindingDB: 7W5O	Ki: 530 (nM) from 1 assay(s)
5ID	BindingDB: 7W5O	IC50: 1200 (nM) from 1 assay(s)
6GI	BindingDB: 7W5O	IC50: 4.70e+4 (nM) from 1 assay(s)