Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.82 kDa 
• Atom Count: 3062 
• Modelled Residue Count: 338 
• Deposited Residue Count: 361 
• Unique protein chains: 1

5BUI

ERK2 complexed with 2-pyridiyl tetrahydroazaindazole

• PDB DOI: 10.2210/pdb5BUI/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-03 Released: 2015-07-15 
• Deposition Author(s): Bellamacina, C.R., Shu, W., Bussiere, D.E., Bagdanoff, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.222 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

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

• PubMed: 26144345 
• DOI: 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.

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Organizational Affiliation: 

Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes for BioMedical Research, 4560 Horton St., Building 4, Emeryville, CA 94608, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	361	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4V9	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	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4V9	Binding MOAD:  5BUI	IC50: 89 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.222 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.83	α = 90
b = 71.25	β = 90
c = 120.06	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-03 
• Released Date: 2015-07-15 
Deposition Author(s): Bellamacina, C.R., Shu, W., Bussiere, D.E., Bagdanoff, J.T.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references, Source and taxonomy