Skip to main content


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 
    0.239 (Depositor) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1MU8

This is version 1.8 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: https://doi.org/10.1021/jm020311f
  • Primary Citation Related Structures: 
    1MU6, 1MU8

  • 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-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

Macromolecule Content 

  • Total Structure Weight: 35.82 kDa 
  • Atom Count: 2,454 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 306 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THROMBIN36Homo 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
THROMBIN259Homo 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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HIRUDIN IIB11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28506 (Hirudo medicinalis)
Explore P28506 
Go to UniProtKB:  P28506
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28506
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on CDB



Download:Ideal Coordinates CCD File
D [auth B]2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-3-METHYL-6-PYRIDINYL)METHYL]ACETAMIDE
C21 H23 F3 N6 O2
WOYBPRBUPLYTPY-UHFFFAOYSA-P
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
C
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work:  0.239 (Depositor) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.12α = 90
b = 72.23β = 100.8
c = 73.03γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2016-05-25
    Changes: Source and taxonomy
  • Version 1.6: 2017-10-11
    Changes: Refinement description
  • Version 1.7: 2021-07-21
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.8: 2024-11-20
    Changes: Data collection, Database references, Structure summary