5BUI

ERK2 complexed with 2-pyridiyl tetrahydroazaindazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4V9Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Ligand efficient tetrahydro-pyrazolopyridines as inhibitors of ERK2 kinase.

Bagdanoff, J.T.Jain, R.Han, W.Poon, D.Lee, P.S.Bellamacina, C.Lindvall, M.

(2015) Bioorg Med Chem Lett 25: 3626-3629

  • DOI: https://doi.org/10.1016/j.bmcl.2015.06.063
  • Primary Citation of Related Structures:  
    5BUE, 5BUI, 5BUJ

  • PubMed Abstract: 

    A series of structure based drug design hypotheses and focused screening efforts drove improvements in the potency and lipophilic efficiency of tetrahydro-pyrazolopyridine based ERK2 inhibitors. Elaboration of a fragment chemical lead established a new lipophilic aryl-Tyr interaction resulting in a substantial potency improvement. Subsequent cleavage of the lipophilic moiety led to reconfiguration of the ligand bound binding cleft. The reconfiguration established a polar contact between a newly liberated N-H and a vicinal Asp, resulting in further improvements in lipophilic efficiency and in vitro clearance.


  • Organizational Affiliation

    Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA. Electronic address: jeffrey.bagdanoff@novartis.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1361Homo sapiensMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4V9
Query on 4V9

Download Ideal Coordinates CCD File 
C [auth A]3-(4-fluorophenyl)-5-(pyridin-2-yl)-4,5,6,7-tetrahydro-2H-pyrazolo[4,3-c]pyridine
C17 H15 F N4
ZJRNBCJAMQCQNC-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.83α = 90
b = 71.25β = 90
c = 120.06γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4V9Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description