3VBX

Exploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in Pim-1 kinase needle screening and inhibitor design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.

Good, A.C.Liu, J.Hirth, B.Asmussen, G.Xiang, Y.Biemann, H.P.Bishop, K.A.Fremgen, T.Fitzgerald, M.Gladysheva, T.Jain, A.Jancsics, K.Metz, M.Papoulis, A.Skerlj, R.Stepp, J.D.Wei, R.R.

(2012) J Med Chem 55: 2641-2648

  • DOI: 10.1021/jm2014698
  • Primary Citation of Related Structures:  
    3VBW, 3VBX, 3VBY, 3VBQ, 3VC4, 3VBT, 3VBV

  • PubMed Abstract: 
  • We have studied the subtleties of fragment docking and binding using data generated in a Pim-1 kinase inhibitor program. Crystallographic and docking data analyses have been undertaken using inhibitor complexes derived from an in-house surface plasmo ...

    We have studied the subtleties of fragment docking and binding using data generated in a Pim-1 kinase inhibitor program. Crystallographic and docking data analyses have been undertaken using inhibitor complexes derived from an in-house surface plasmon resonance (SPR) fragment screen, a virtual needle screen, and a de novo designed fragment inhibitor hybrid. These investigations highlight that fragments that do not fill their binding pocket can exhibit promiscuous hydrophobic interactions due to the lack of steric constraints imposed on them by the boundaries of said pocket. As a result, docking modes that disagree with an observed crystal structure but maintain key crystallographically observed hydrogen bonds still have potential value in ligand design and optimization. This observation runs counter to the lore in fragment-based drug design that all fragment elaboration must be based on the parent crystal structure alone.


    Organizational Affiliation

    Department of Medicinal Chemistry, Genzyme Corp., 153 Second Avenue, Waltham, Massachusetts 02451, United States. andrew.good@genzyme.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A299Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0FO
Query on 0FO

Download CCD File 
A
6-bromo-4-hydroxy-2H-chromen-2-one
C9 H5 Br O3
KNMCTCABMSGXGR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0FOIC50 :  17000   nM  PDBBind
0FOIC50:  17000   nM  BindingDB
0FOIC50:  17000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97α = 90
b = 97β = 90
c = 81γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-01-02 
  • Released Date: 2012-03-21 
  • Deposition Author(s): Liu, J.

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-16
    Changes: Database references
  • Version 1.2: 2018-06-06
    Changes: Data collection