5EGM

Development of a novel tricyclic class of potent and selective FIXa inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb5EGM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-27 Released: 2015-11-18 
• Deposition Author(s): Meng, D., Andre, P., Bateman, T.J., Berger, R., Chen, Y., Desai, K., Dewnani, S., Ellsworth, K., Feng, D., Geissler, W.M., Guo, L., Hruza, A., Jian, T., Li, H., Parker, D.L., Reichert, P., Sherer, E.C., Smith, C.J., Sonatore, L.M., Tschirret-Guth, R., Wu, J., Xu, J., Zhang, T., Campeau, L., Orr, R., Poirier, M., McCabe-Dunn, j., Araki, K., Nishimura, T., Sakurada, I., Hirabayashi, T., Wood, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.171 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

Development of a novel tricyclic class of potent and selective FIXa inhibitors.

Meng, D., Andre, P., Bateman, T.J., Berger, R., Chen, Y.H., Desai, K., Dewnani, S., Ellsworth, K., Feng, D., Geissler, W.M., Guo, L., Hruza, A., Jian, T., Li, H., Metzger, J., Parker, D.L., Reichert, P., Sherer, E.C., Smith, C.J., Sonatore, L.M., Tschirret-Guth, R., Wu, J., Xu, J., Zhang, T., Campeau, L.C., Orr, R., Poirier, M., McCabe-Dunn, J., Araki, K., Nishimura, T., Sakurada, I., Hirabayashi, T., Wood, H.B.

(2015) Bioorg Med Chem Lett 25: 5437-5443

• PubMed: 26318999 
• DOI: https://doi.org/10.1016/j.bmcl.2015.07.078
• Primary Citation of Related Structures:  
  5EGM


• PubMed Abstract: 
  

Using structure based drug design, a novel class of potent coagulation factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds were evaluated in rat IV/PO pharmacokinetic (PK) studies and demonstrated desirable oral PK profiles. Finally, the pharmacodynamics (PD) of this class of molecules were evaluated in thrombin generation assay (TGA) in Corn Trypsin Inhibitor (CTI) citrated human plasma and demonstrated characteristics of a FIXa inhibitor.

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Organizational Affiliation: 

Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.

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: 33.73 kDa 
• Atom Count: 2,565 
• Modelled Residue Count: 289 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A	235	Homo sapiens	Mutation(s): 1  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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NY	E [auth A]	2-chloranyl-~{N}-[(7~{S})-2-methyl-7-phenyl-10-(1~{H}-1,2,3,4-tetrazol-5-yl)-8,9-dihydro-6~{H}-pyrido[1,2-a]indol-7-yl]-4-(1,2,4-triazol-4-yl)benzamide C29 H24 Cl N9 O TUCDMISJVGVBLL-GDLZYMKVSA-N
NHE	D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5NY	Binding MOAD:  5EGM	Ki: 2.4 (nM) from 1 assay(s)
	BindingDB:  5EGM	IC50: 2.38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.171 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.298	α = 90
b = 99.298	β = 90
c = 94.685	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data scaling
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Meng, D., Andre, P., Bateman, T.J., Berger, R., Chen, Y., Desai, K., Dewnani, S., Ellsworth, K., Feng, D., Geissler, W.M., Guo, L., Hruza, A., Jian, T., Li, H., Parker, D.L., Reichert, P., Sherer, E.C., Smith, C.J., Sonatore, L.M., Tschirret-Guth, R., Wu, J., Xu, J., Zhang, T., Campeau, L., Orr, R., Poirier, M., McCabe-Dunn, j., Araki, K., Nishimura, T., Sakurada, I., Hirabayashi, T., Wood, H.B.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description