1TX7

Bovine Trypsin complexed with p-amidinophenylmethylphosphinic acid (AMPA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

An oxyanion-hole selective serine protease inhibitor in complex with trypsin.

Cui, J., Marankan, F., Fu, W., Crich, D., Mesecar, A., Johnson, M.E.

(2002) Bioorg Med Chem 10: 41-46

  • DOI: 10.1016/s0968-0896(01)00259-0
  • Primary Citation of Related Structures:  
    1TX7

  • PubMed Abstract: 

    • p-amidinophenylmethylphosphinic acid (AMPA) was designed, synthesized and crystallized in complex with trypsin to study interactions with the oxyanion hole at the S1 site. In comparison to benzamidine, AMPA shows improved activity, which the crystal structure demonstrates to result from hydrogen bonds between the negatively charged phosphinic acid group and the catalytic residues at the oxyanion hole ...

    p-amidinophenylmethylphosphinic acid (AMPA) was designed, synthesized and crystallized in complex with trypsin to study interactions with the oxyanion hole at the S1 site. In comparison to benzamidine, AMPA shows improved activity, which the crystal structure demonstrates to result from hydrogen bonds between the negatively charged phosphinic acid group and the catalytic residues at the oxyanion hole.

    Organizational Affiliation: 

    Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Avenue, M/C 870, Chicago, IL 60607-7173, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TrypsinogenA223Bos 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4CM
Query on 4CM
Download Ideal Coordinates CCD File 
C [auth A](4-CARBAMIMIDOYLPHENYL)-METHYL-PHOSPHINIC ACID
C8 H11 N2 O2 P
CVABPMXIKVDCLF-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
4CM Binding MOAD:  1TX7 Ki: 2.50e+4 (nM) from 1 assay(s)
PDBBind:  1TX7 Ki: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.87α = 90
b = 58.44β = 90
c = 67.52γ = 90

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection