Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.17 kDa 
• Atom Count: 1801 
• Residue Count: 223 
• Unique protein chains: 1

1TNG

PREDICTION OF NOVEL SERINE PROTEASE INHIBITORS

• DOI: 10.2210/pdb1TNG/pdb

• Classification: HYDROLASE/hydrolase inhibitor
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1994-07-21 Released: 1994-11-30 
• Deposition Author(s): Kurinov, I., Harrison, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

Prediction of new serine proteinase inhibitors.

Kurinov, I.V., Harrison, R.W.

(1994) Nat Struct Biol 1: 735-743

• PubMed: 7634078 
• DOI: 10.1038/nsb1094-735
• Primary Citation of Related Structures:  
  1TNJ, 1TNI, 1TNH, 1TNG, 1TNL, 1TNK


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN	A	229	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMC	A	AMINOMETHYLCYCLOHEXANE C7 H16 N AVKNGPAMCBSNSO-UHFFFAOYSA-O
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AMC	Ki :  1170000   nM  PDBBind
AMC	Ki:  1170000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.946	α = 90
b = 58.424	β = 90
c = 67.581	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-21 
• Released Date: 1994-11-30 
Deposition Author(s): Kurinov, I., Harrison, R.W.

Revision History 

• 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