6X5J

Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of hydroxy pyrimidine Factor IXa inhibitors.

Jayne, C.L.Andreani, T.Chan, T.Y.Chelliah, M.V.Clasby, M.C.Dwyer, M.Eagen, K.A.Fried, S.Greenlee, W.J.Guo, Z.Hawes, B.Hruza, A.Ingram, R.Keertikar, K.M.Neelamkavil, S.Reichert, P.Xia, Y.Chackalamannil, S.

(2020) Bioorg Med Chem Lett 30: 127279-127279

  • DOI: 10.1016/j.bmcl.2020.127279
  • Primary Citation of Related Structures:  
    6X5L, 6X5P, 6X5J

  • PubMed Abstract: 
  • The synthesis and structure activity relationship development of a pyrimidine series of heterocyclic Factor IXa inhibitors is described. Increased selectivity over Factor Xa inhibition was achieved through SAR expansion of the P1 element. Select compounds were evaluated in vivo to assess their plasma levels in rat ...

    The synthesis and structure activity relationship development of a pyrimidine series of heterocyclic Factor IXa inhibitors is described. Increased selectivity over Factor Xa inhibition was achieved through SAR expansion of the P1 element. Select compounds were evaluated in vivo to assess their plasma levels in rat.


    Organizational Affiliation

    Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXA235Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXB62Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6NH
Query on 6NH

Download Ideal Coordinates CCD File 
E [auth A]2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
C17 H14 N6 O
CKSIVONWCYACAP-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.548α = 90
b = 100.548β = 90
c = 98.495γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release