7W5O

Crystal structure of ERK2 with an allosteric inhibitor


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1
A, B
368Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6GI
Query on 6GI

Download Ideal Coordinates CCD File 
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
5ID
Query on 5ID

Download Ideal Coordinates CCD File 
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
EPE
Query on EPE

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
TAR
Query on TAR

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L [auth B]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
SIN
Query on SIN

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E [auth A],
G [auth A]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
MLA
Query on MLA

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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
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP
A, B
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Binding Affinity Annotations 
IDSourceBinding Affinity
5ID BindingDB:  7W5O Ki: 530 (nM) from 1 assay(s)
IC50: 1200 (nM) from 1 assay(s)
6GI BindingDB:  7W5O IC50: 4.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.812α = 90
b = 82.812β = 90
c = 274.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description