1MUE

Thrombin-Hirugen-L405,426


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Pharmacokinetic optimization of 3-amino-6-chloropyrazinone acetamide thrombin inhibitors. Implementation of P3 pyridine N-oxides to deliver an orally bioavailable series containing P1 N-benzylamides.

Burgey, C.S.Robinson, K.A.Lyle, T.A.Nantermet, P.G.Selnick, H.G.Isaacs, R.C.Lewis, S.D.Lucas, B.J.Krueger, J.A.Singh, R.Miller-Stein, C.White, R.B.Wong, B.Lyle, E.A.Stranieri, M.T.Cook, J.J.McMasters, D.R.Pellicore, J.M.Pal, S.Wallace, A.A.Clayton, F.C.Bohn, D.Welsh, D.C.Lynch, J.J.Yan, Y.Chen, Z.Kuo, L.Gardell, S.J.Shafer, J.A.Vacca, J.P.

(2003) Bioorg Med Chem Lett 13: 1353-1357

  • DOI: 10.1016/s0960-894x(03)00099-4
  • Primary Citation of Related Structures:  
    1MUE

  • PubMed Abstract: 
  • In this manuscript we demonstrate that a modification principally directed toward the improvement of the aqueous solubility (i.e., introduction a P3 pyridine N-oxide) of the previous lead compound afforded a new series of potent orally bioavailable P ...

    In this manuscript we demonstrate that a modification principally directed toward the improvement of the aqueous solubility (i.e., introduction a P3 pyridine N-oxide) of the previous lead compound afforded a new series of potent orally bioavailable P1 N-benzylamide thrombin inhibitors. An expedited investigation of the P1 SAR with respect to oral bioavailability, plasma half-life, and human liver microsome stability revealed 5 as the best candidate for advanced evaluation.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINA36Homo 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBINB259Homo 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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUDIN IIBC11Hirudo 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
CDD
Query on CDD

Download CCD File 
B
2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDO-2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUOROPHENYL)METHYL]ACETAMIDE
C20 H17 Cl F3 N5 O3
ZIGSBBKEPNQXRG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
CL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CDDKi :  2.299999952316284   nM  PDBBind
CDDKi:  2.299999952316284   nM  Binding MOAD
CDDKi:  2.299999952316284   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.01α = 90
b = 72.11β = 100.66
c = 72.84γ = 90

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    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