1AUJ

BOVINE TRYPSIN COMPLEXED TO META-CYANO-BENZYLIC INHIBITOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

New inhibitors of thrombin and other trypsin-like proteases: hydrogen bonding of an aromatic cyano group with a backbone amide of the P1 binding site replaces binding of a basic side chain.

Lee, S.L., Alexander, R.S., Smallwood, A., Trievel, R., Mersinger, L., Weber, P.C., Kettner, C.

(1997) Biochemistry 36: 13180-13186

  • DOI: 10.1021/bi970912m

  • PubMed Abstract: 

    • Highly effective thrombin inhibitors have been obtained by preparing boronic acid analogues of m-cyano-substituted phenylalanine and its incorporation into peptides. The cyano group enhances binding by several orders of magnitude. For example, Ac-(D) ...

    Highly effective thrombin inhibitors have been obtained by preparing boronic acid analogues of m-cyano-substituted phenylalanine and its incorporation into peptides. The cyano group enhances binding by several orders of magnitude. For example, Ac-(D)Phe-Pro-boroPheOH binds to thrombin with a Ki of 320 nM and the Ki of Ac-(D)Phe-Pro-boroPhe(m-CN)-OH is 0.79 nM. Protein crystal structure determination of trypsin complexed to H-(D)Phe-Pro-boroPhe(m-CN)-OH indicates that the aromatic side chain is bound in the P1 binding site and that the cyano group can act as a H-bond acceptor for the amide proton of Gly219. Enhanced binding for inhibitors containing the m-cyano group was observed for coagulation factor Xa and for the factor VIIa.tissue factor complex [Ki values of Ac-(D)Phe-Pro-boroPhe(mCN)-OH are 760 and 3.3 nM, respectively]. This result is consistent with the sequence homology of these two enzymes in the P1 binding site. Two enzymes lacking the strict homology in the P1 binding site, pancreatic kallikrein and chymotrypsin, did not exhibit significantly enhanced binding.

    Related Citations: 
    • Kinetic and Crystallographic Studies of Thrombin with Ac-(D)Phe-Pro-Boroarg-Oh and its Lysine, Amidine, Homolysine, and Ornithine Analogs
      Weber, P.C.,Lee, S.L.,Lewandowski, F.A.,Schadt, M.C.,Chang, C.W.,Kettner, C.A.
      (1995) Biochemistry 34: 3750
    • The Single Calcium-Binding Site of Crystallin Bovin Beta-Trypsin
      Bode, W.,Schwager, P.
      (1975) FEBS Lett. 56: 139
    • The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 A Resolution. I. Crystallization, Data Collection and Application of Patterson Search Technique
      Fehlhammer, H.,Bode, W.
      (1975) J.Mol.Biol. 98: 683

    Organizational Affiliation: 

    Chemical and Physical Sciences, DuPont Merck Pharmaceutical Company, P. O. Box 80500, Wilmington, Delaware 19880-0500, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPB
Query on PPB
Download SDF File 
Download CCD File 
A
1-{[1-(2-AMINO-3-PHENYL-PROPIONYL)-PYRROLIDINE-2-CARBONYL]-AMINO}-2-(3-CYANO-PHENYL)-ETHANEBORONIC ACID
(D)PHE-PRO-BOROPHE(M-CN)
C23 H27 B N4 O4
UFOIPTZMXQILSG-HKBOAZHASA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPBKi: 5.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.000α = 90.00
b = 58.400β = 90.00
c = 67.600γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORrefinement
R-AXISdata collection
X-PLORmodel building
X-PLORphasing
R-AXISdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance