7X4U

Crystal structure of ERK2 with an allosteric inhibitor 2

PDB DOI: https://doi.org/10.2210/pdb7X4U/pdb

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

Deposited: 2022-03-03 Released: 2023-03-08
Deposition Author(s): Yoshida, M., Kinoshita, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199

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

Structural basis for producing allosteric ERK2 inhibitors

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

To be published.

Macromolecule Content

Total Structure Weight: 43.64 kDa
Atom Count: 3,194
Modelled Residue Count: 350
Deposited Residue Count: 368
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	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8DK Query on 8DK 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]	N-(1,3-benzodioxol-5-ylmethyl)-2-[3-(3,4-dimethylphenyl)-7-oxidanylidene-[1,2,3]triazolo[4,5-d]pyrimidin-6-yl]ethanamide C₂₂ H₂₀ N₆ O₄ ZUYKNWLWIGKTSN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
5ID Query on 5ID Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [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 B [auth A] Interactions & Density Focus chain B [auth A]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5ID	BindingDB: 7X4U	Ki: 530 (nM) from 1 assay(s)
5ID	BindingDB: 7X4U	IC50: 1200 (nM) from 1 assay(s)
8DK	BindingDB: 7X4U	IC50: 1.10e+4 (nM) from 1 assay(s)