1Z71

thrombin and P2 pyridine N-oxide inhibitor complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

P(2) pyridine N-oxide thrombin inhibitors: a novel peptidomimetic scaffold

Nantermet, P.G.Burgey, C.S.Robinson, K.A.Pellicore, J.M.Newton, C.L.Deng, J.Z.Selnick, H.G.Lewis, S.D.Lucas, B.J.Krueger, J.A.Miller-Stein, C.White, R.B.Wong, B.McMasters, D.R.Wallace, A.A.Lynch Jr., J.J.Yan, Y.Chen, Z.Kuo, L.Gardell, S.J.Shafer, J.A.Vacca, J.P.Lyle, T.A.

(2005) Bioorg Med Chem Lett 15: 2771-2775

  • DOI: 10.1016/j.bmcl.2005.03.110
  • Primary Citation of Related Structures:  
    1Z71

  • PubMed Abstract: 
  • In this study, we have demonstrated that the critical hydrogen bonding motif of the established 3-aminopyrazinone thrombin inhibitors can be effectively mimicked by a 2-aminopyridine N-oxide. As this peptidomimetic core is more resistant toward oxida ...

    In this study, we have demonstrated that the critical hydrogen bonding motif of the established 3-aminopyrazinone thrombin inhibitors can be effectively mimicked by a 2-aminopyridine N-oxide. As this peptidomimetic core is more resistant toward oxidative metabolism, it also overcomes the metabolic liability associated with the pyrazinones. An optimization study of the P(1) benzylamide delivered the potent thrombin inhibitor 21 (K(i) = 3.2 nM, 2xaPTT = 360 nM), which exhibited good plasma levels and half-life after oral dosing in the dog (C(max) = 2.6 microM, t(1/2) = 4.5 h).


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. philippe_nantermet@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thrombinA287Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hirudin IIIB'B11Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L17
Query on L17

Download CCD File 
A
L17
C22 H20 Cl2 F2 N4 O3
ISTCYDGUBPNUDF-CQSZACIVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
BL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L17Ki:  0.6600000262260437   nM  Binding MOAD
L17Ki :  0.6600000262260437   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.97α = 90
b = 71.49β = 100.5
c = 72.26γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-03-13
    Changes: Other
  • Version 1.5: 2017-10-11
    Changes: Refinement description