5V62

Phospho-ERK2 bound to bivalent inhibitor SBP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Guided Strategy for the Development of Potent Bivalent ERK Inhibitors.

Lechtenberg, B.C.Mace, P.D.Sessions, E.H.Williamson, R.Stalder, R.Wallez, Y.Roth, G.P.Riedl, S.J.Pasquale, E.B.

(2017) ACS Med Chem Lett 8: 726-731


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
351Homo sapiensMutation(s): 0 
Gene Names: MAPK1 (ERK2, PRKM1, PRKM2)
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Go to Gene View: MAPK1
Go to UniProtKB:  P28482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S6 kinase alpha-1
I
21Homo sapiensMutation(s): 0 
Gene Names: RPS6KA1 (MAPKAPK1A, RSK1)
EC: 2.7.11.1
Find proteins for Q15418 (Homo sapiens)
Go to Gene View: RPS6KA1
Go to UniProtKB:  Q15418
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AKS
Query on AKS

Download SDF File 
Download CCD File 
A
N-(hex-5-yn-1-yl)hexanamide
C12 H21 N O
CJZDJNGNVAVPMZ-UHFFFAOYSA-N
 Ligand Interaction
FRZ
Query on FRZ

Download SDF File 
Download CCD File 
A
5-(2-PHENYLPYRAZOLO[1,5-A]PYRIDIN-3-YL)-1H-PYRAZOLO[3,4-C]PYRIDAZIN-3-AMINE
FR180204
C18 H13 N7
XVECMUKVOMUNLE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
AZK
Query on AZK
I
L-PEPTIDE LINKINGC6 H14 N4 OLYS
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.327α = 90.00
b = 77.888β = 90.00
c = 152.938γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA160457

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2018-04-18
    Type: Advisory, Data collection, Database references