4ABE

Fragments bound to bovine trypsin for the SAMPL challenge


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


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:  
    4ABE, 4ABF, 4ABG, 4ABH, 4ABA, 4ABB, 4ABD, 4AB8, 4AB9

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CATIONIC TRYPSINA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
913
Query on 913

Download CCD File 
A
(3-PYRAZOL-1-YLPHENYL)METHANAMINE
C10 H11 N3
YWZKZHCZKIKAAC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
913Kd :  400000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.37α = 90
b = 58.648β = 90
c = 66.453γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

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