6X5L

Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6X5L/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-26 Released: 2020-06-24 
• Deposition Author(s): Jayne, C.L., Andreani, T., Chan, T., 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.

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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 

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

• PubMed: 32527459 
• 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.

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Organizational Affiliation: 

Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.23 kDa 
• Atom Count: 2,443 
• Modelled Residue Count: 282 
• Deposited Residue Count: 296 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A	234	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B	62	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQG (Subject of Investigation/LOI)	C [auth A]	4-{[5-hydroxy-6-(4-methylphenyl)pyrimidin-4-yl]amino}benzene-1-carboximidamide C18 H17 N5 O FQSMNGLHSXWGEE-UHFFFAOYSA-N
CIT	E [auth A], F [auth A], G [auth A], H [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 100.56	α = 90
b = 100.56	β = 90
c = 98.202	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
autoBUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Jayne, C.L., Andreani, T., Chan, T., 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.

Revision History  

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