1MU6

Crystal Structure of Thrombin in Complex with L-378,622


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines.

Burgey, C.S.Robinson, K.A.Lyle, T.A.Sanderson, P.E.Lewis, S.D.Lucas, B.J.Krueger, J.A.Singh, R.Miller-Stein, C.White, R.B.Wong, B.Lyle, E.A.Williams, P.D.Coburn, C.A.Dorsey, B.D.Barrow, J.C.Stranieri, M.T.Holahan, M.A.Sitko, G.R.Cook, J.J.McMasters, D.R.McDonough, C.M.Sanders, W.M.Wallace, A.A.Clayton, F.C.Bohn, D.Leonard, Y.M.Detwiler Jr., T.J.Lynch Jr., J.J.Yan, Y.Chen, Z.Kuo, L.Gardell, S.J.Shafer, J.A.Vacca, J.P.J.

(2003) J Med Chem 46: 461-473

  • DOI: 10.1021/jm020311f
  • Primary Citation of Related Structures:  
    1MU8, 1MU6

  • PubMed Abstract: 
  • Recent efforts in the field of thrombin inhibitor research have focused on the identification of compounds with good oral bioavailability and pharmacokinetics. In this manuscript we describe a metabolism-based approach to the optimization of the 3-(2 ...

    Recent efforts in the field of thrombin inhibitor research have focused on the identification of compounds with good oral bioavailability and pharmacokinetics. In this manuscript we describe a metabolism-based approach to the optimization of the 3-(2-phenethylamino)-6-methylpyrazinone acetamide template (e.g., 1) which resulted in the modification of each of the three principal components (i.e., P1, P2, P3) comprising this series. As a result of these studies, several potent thrombin inhibitors (e.g., 20, 24, 25) were identified which exhibit high levels of oral bioavailability and long plasma half-lives.


    Organizational Affiliation

    Departments of Medicinal Chemistry, Biological Chemistry, Drug Metabolism, Molecular Systems, Structural Biology, and Pharmacology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA. christopher_burgey@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
CDA
Query on CDA

Download CCD File 
B
2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-6-PYRIDINYL)METHYL]ACETAMIDE
C20 H19 F3 N6 O2
JXHWVKOKYDAROD-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 %)
CDAKi:  4.199999809265137   nM  BindingDB
CDAKi:  4.199999809265137   nM  Binding MOAD
CDAKi :  4.199999809265137   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.22α = 90
b = 72.21β = 101.1
c = 73.3γ = 90
Software Package:
Software NamePurpose
CNXrefinement

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