5VUC

Pim1 Kinase in complex with a benzofuranone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach

Watanabe, C.Watanabe, H.Fukuzawa, K.Parker, L.J.Okiyama, Y.Yuki, H.Yokoyama, S.Nakano, H.Tanaka, S.Honma, T.

(2017) J Chem Inf Model 57: 2996-3010

  • DOI: https://doi.org/10.1021/acs.jcim.7b00110
  • Primary Citation of Related Structures:  
    5VUA, 5VUB, 5VUC

  • PubMed Abstract: 

    Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson-Boltzmann surface area (FMO+MM-PBSA) approach. This methodology enables quantum-chemical calculations for large biomolecules with solvation. In the course of drug discovery targeting Pim1, six benzofuranone-class inhibitors were found to differ only in the position of the indole-ring nitrogen atom. By comparing the various qualities of complex structures based on X-ray, classical molecular mechanics (MM)-optimized, and quantum/molecular mechanics (QM/MM)-optimized structures, we found that the QM/MM-optimized structures provided the best correlation (R 2 = 0.85) between pIC 50 and the calculated FMO+MM-PBSA binding energy. Combining the classical solvation energy with the QM binding energy was important to increase the correlation. In addition, decomposition of the interaction energy into various physicochemical components by pair interaction energy decomposition analysis suggested that CH-π and electrostatic interactions mainly caused the activity differences.


  • Organizational Affiliation

    RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A [auth B]298Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8GR
Query on 8GR

Download Ideal Coordinates CCD File 
C [auth B](2Z)-2-(1H-indol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3-one
C23 H23 N3 O3
ZSHOEUJOJHPBFX-MTJSOVHGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A [auth B]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
8GR BindingDB:  5VUC IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.37α = 90
b = 98.37β = 90
c = 80.68γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2017-12-13 
  • Deposition Author(s): Parker, L.J.

Funding OrganizationLocationGrant Number
JSPS KAKENHIJapanJP15582248

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references