1Z71 | pdb_00001z71

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 (Depositor) 
  • R-Value Work: 
    0.223 (Depositor) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1Z71

This is version 1.6 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: https://doi.org/10.1016/j.bmcl.2005.03.110
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 35.01 kDa 
  • Atom Count: 2,564 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 298 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
thrombin287Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hirudin IIIB'11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28504
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L17

Query on L17



Download:Ideal Coordinates CCD File
C [auth A]L17
C22 H20 Cl2 F2 N4 O3
ISTCYDGUBPNUDF-CQSZACIVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.254 (Depositor) 
  • R-Value Work:  0.223 (Depositor) 
  • R-Value Observed: 0.223 (Depositor) 
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  (Full details and data files)

  • 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
  • Version 1.6: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary