4RPV | pdb_00004rpv

co-crystal structure of Pim1 with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.273 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.200 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3URClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

The discovery of novel 3-(pyrazin-2-yl)-1H-indazoles as potent pan-Pim kinase inhibitors.

Wang, H.L.Cee, V.J.Chavez, F.Lanman, B.A.Reed, A.B.Wu, B.Guerrero, N.Lipford, J.R.Sastri, C.Winston, J.Andrews, K.L.Huang, X.Lee, M.R.Mohr, C.Xu, Y.Zhou, Y.Tasker, A.S.

(2015) Bioorg Med Chem Lett 25: 834-840

  • DOI: https://doi.org/10.1016/j.bmcl.2014.12.068
  • Primary Citation of Related Structures:  
    4RPV, 4WRS

  • PubMed Abstract: 

    The three Pim kinases are a small family of serine/threonine kinases regulating several signaling pathways that are fundamental to tumorigenesis. As such, the Pim kinases are a very attractive target for pharmacological inhibition in cancer therapy. Herein, we describe our efforts toward the development of a potent, pan-Pim inhibitor. The synthesis and hit-to-lead SAR development from a 3-(pyrazin-2-yl)-1H-indazole derived hit 2 to the identification of a series of potent, pan-Pim inhibitors such as 13o are described.


  • Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: huiw@amgen.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1410Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3UR
Query on 3UR

Download Ideal Coordinates CCD File 
B [auth A](3S)-1-{6-[5-(2,6-difluorophenyl)-2H-indazol-3-yl]pyrazin-2-yl}piperidin-3-amine
C22 H20 F2 N6
HWIDISMNBLRQNP-AWEZNQCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.273 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.200 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.091α = 90
b = 100.091β = 90
c = 81.205γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3URClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2015-02-04 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations