5EGM | pdb_00005egm

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 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.148 (Depositor) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

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 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. Electronic address: [e-mail].
Department of Cardiometabolic Disease, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Pharmacokinetics, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Pharmacology, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Structural Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Chemistry Modeling and Informatics, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Department of Process Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.
Discovery Research, Mochida Pharmaceutical Co., LTD, 7, Yotsuya 1-Chome, Shinjuku-ku, Tokyo 160-8515, Japan.

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 
• Modeled 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 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 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.171 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.148 (Depositor) 
• R-Value Observed: 0.149 (Depositor) 

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
• Version 1.3: 2024-11-20
  Changes: Structure summary