4QTB

Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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Literature

A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics.

Chaikuad, A., M C Tacconi, E., Zimmer, J., Liang, Y., Gray, N.S., Tarsounas, M., Knapp, S.

(2014) Nat Chem Biol 10: 853-860

  • DOI: https://doi.org/10.1038/nchembio.1629
  • Primary Citation of Related Structures:  
    4QTA, 4QTB, 4QTC, 4QTD, 4QTE

  • PubMed Abstract: 

    • Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity ...

    Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity. In ERK1/2, SCH772984 induces a so-far-unknown binding pocket that accommodates the piperazine-phenyl-pyrimidine decoration. This new binding pocket was created by an inactive conformation of the phosphate-binding loop and an outward tilt of helix αC. In contrast, structure determination of SCH772984 with the off-target haspin and JNK1 revealed two canonical but distinct type I binding modes. Notably, the new binding mode with ERK1/2 was associated with slow binding kinetics in vitro as well as in cell-based assay systems. The described binding mode of SCH772984 with ERK1/2 enables the design of a new type of specific kinase inhibitors with prolonged on-target activity.

    Organizational Affiliation: 

    1] Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK. [2] Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA. [3] Target Discovery Institute, University of Oxford, Nuffield Department of Medicine Research Building, Oxford, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 3
A, B
380Homo sapiensMutation(s): 0 
Gene Names: ERK1, MAPK3, PRKM3
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P27361 (Homo sapiens)
Explore P27361 
Go to UniProtKB:  P27361
PHAROS:  P27361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27361
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
38Z
Query on 38Z
Download Ideal Coordinates CCD File 
FA [auth B],
T [auth A]		(3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide
C33 H33 N9 O2
HDAJDNHIBCDLQF-RUZDIDTESA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
EA [auth B],
S [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
BA [auth B],
P [auth A],
Q [auth A]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
CA [auth B],
DA [auth B],
R [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
38Z Binding MOAD:  4QTB Kd: 213 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.98α = 90
b = 94.01β = 91.71
c = 65.36γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references