6X5L

Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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

  • 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.


  • Organizational Affiliation

    Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA. Electronic address: Charles.Jayne@merck.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor IX234Homo 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
GTEx:  ENSG00000101981 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor IX62Homo 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
GTEx:  ENSG00000101981 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQG (Subject of Investigation/LOI)
Query on UQG

Download Ideal Coordinates CCD File 
C [auth A]4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide
C18 H17 N5 O
FQSMNGLHSXWGEE-UHFFFAOYSA-N
CIT
Query on CIT

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

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UQG BindingDB:  6X5L IC50: 44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.56α = 90
b = 100.56β = 90
c = 98.202γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
autoBUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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