1Z71

thrombin and P2 pyridine N-oxide inhibitor complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thrombin
A
287Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hirudin IIIB'
B
11Hirudo medicinalisMutation(s): 0 
Find proteins for P28511 (Hirudo medicinalis)
Go to UniProtKB:  P28511
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L17
Query on L17

Download SDF File 
Download CCD File 
A
L17
2-(3-CHLORO-6-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-1-OXIDOPYRIDIN-2-YL)-N-[1-(3-CHLOROPHENYL)ETHYL]ACETAMIDE
C22 H20 Cl2 F2 N4 O3
ISTCYDGUBPNUDF-CQSZACIVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L17Ki: 0.66 nM BINDINGMOAD
L17Ki: 0.66 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.970α = 90.00
b = 71.490β = 100.50
c = 72.260γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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