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

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 

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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: https://doi.org/10.1021/jm2014698
  • Primary Citation of Related Structures:  
    3VBQ, 3VBT, 3VBV, 3VBW, 3VBX, 3VBY, 3VC4

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1299Homo sapiensMutation(s): 0 
Gene Names: PIM1
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
0FS PDBBind:  3VC4 IC50: 24 (nM) from 1 assay(s)
Binding MOAD:  3VC4 IC50: 24 (nM) from 1 assay(s)
BindingDB:  3VC4 IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.260 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.496α = 90
b = 98.496β = 90
c = 81.025γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-16
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations