1TNK

PREDICTION OF NOVEL SERINE PROTEASE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Prediction of new serine proteinase inhibitors.

Kurinov, I.V.Harrison, R.W.

(1994) Nat Struct Biol 1: 735-743

  • DOI: 10.1038/nsb1094-735
  • Primary Citation of Related Structures:  
    1TNG, 1TNH, 1TNI, 1TNJ, 1TNK, 1TNL

  • PubMed Abstract: 
  • We describe here the use of a rapid computational method to predict the relative binding strengths of a series of small-molecule ligands for the serine proteinase trypsin. Flexible molecular models of the ligands were docked to the proteinase using an all-atom potential set, without cutoff limits for the non-bonded and electrostatic energies ...

    We describe here the use of a rapid computational method to predict the relative binding strengths of a series of small-molecule ligands for the serine proteinase trypsin. Flexible molecular models of the ligands were docked to the proteinase using an all-atom potential set, without cutoff limits for the non-bonded and electrostatic energies. The binding-strength calculation is done directly in terms of a molecular mechanics potential. The binding of eighteen different compounds, including non-binding controls, has been successfully predicted. The measured Ki is correlated with the predicted energy. The correctness of the theoretical calculations is demonstrated with both kinetics measurements and X-ray structure determination of six enzyme-inhibitor complexes.


    Organizational Affiliation

    Department of Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSINA229Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRA
Query on PRA

Download Ideal Coordinates CCD File 
C [auth A]3-PHENYLPROPYLAMINE
C9 H13 N
LYUQWQRTDLVQGA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PRA Binding MOAD:  1TNK Ki: 3.25e+7 (nM) from 1 assay(s)
PDBBind:  1TNK Ki: 3.25e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.948α = 90
b = 58.459β = 90
c = 67.652γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-05-06
    Changes: Non-polymer description, Other, Structure summary