4AB8

Fragments bound to bovine trypsin for the SAMPL challenge

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

The Dingo Dataset: A Comprehensive Set of Data for the Sampl Challenge.

Newman, J., Dolezal, O., Fazio, V., Caradoc-Davies, T., Peat, T.S.

(2012) J Comput Aided Mol Des 26: 497

  • DOI: 10.1007/s10822-011-9521-2
  • Primary Citation of Related Structures:  
    4AB8, 4AB9, 4ABA, 4ABB, 4ABD, 4ABE, 4ABF, 4ABG, 4ABH

  • PubMed Abstract: 

    • Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques ...

    Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies.

    Related Citations: 
    • Practical Aspects of the Sampl Challenge: Providing an Extensive Experimental Data Set for the Modeling Community.
      Newman, J., Fazio, V.J., Caradoc-Davies, T.T., Branson, K., Peat, T.S.
      (2009) J Biomol Screen 14: 1245
    • Fragment Screening for the Modelling Community: Spr, Itc, and Crystallography
      Dolezal, O., Doughty, L., Hattarki, M.K., Fazio, V.J., Caradoc-Davies, T.T., Newman, J., Peat, T.S.
      (2013) Aust J Chem 66: 1507
    Organizational Affiliation: 

    CSIRO Division of Materials, Science and Engineering, 343 Royal Parade, Parkville, VIC 3052, Australia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATIONIC TRYPSINA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VXU
Query on VXU
Download Ideal Coordinates CCD File 
I [auth A]3,4-dihydro-2H-1,5-benzodioxepin-6-ylmethanamine
C10 H13 N O2
ZXJOKQNPRXXPJT-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VXU PDBBind:  4AB8 Kd: 1.36e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.323α = 90
b = 54.323β = 90
c = 105.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-12-08 
  • Released Date: 2012-02-08 
    • Deposition Author(s): Newman, J., Peat, T.S.

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references