Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 33.68 kDa 
• Atom Count: 2567 
• Modelled Residue Count: 289 
• Deposited Residue Count: 297 
• Unique protein chains: 2

4ZAE

Development of a novel class of potent and selective FIXa inhibitors

• DOI: 10.2210/pdb4ZAE/pdb

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


• Deposited: 2015-04-13 Released: 2015-06-03 
• Deposition Author(s): Hruza, A., Reichert, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.174 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

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

Zhang, T., Andre, P., Bateman, T.J., Chen, Y.H., Desai, K., Ellsworth, K., Geissler, W.M., Guo, L., Hruza, A., Jian, T., Meng, D., Parker, D.L., Qian, X., Reichert, P., Sherer, E.C., Shu, M., Smith, C.J., Sonatore, L.M., Tschirret-Guth, R., Nolting, A.F., Orr, R., Campeau, L.C., Araki, K., Nishimura, T., Sakurada, I., Wood, H.B.

(2015) Bioorg Med Chem Lett 25: 4945-4949

• PubMed: 25978966 
• DOI: 10.1016/j.bmcl.2015.04.057
• Primary Citation of Related Structures:  
  4ZAE


• PubMed Abstract: 
  

Using structure based drug design (SBDD), a novel class of potent coagulation Factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds demonstrated oral bioavailability in rat IV/PO pharmacokinetic (PK) studies. Finally, the pharmacodynamics (PD) of this class of molecules was 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 Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.

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
4M1	C [auth A]	2,6-dichloro-N-[(2R)-2-(5,6-dimethyl-1H-benzimidazol-2-yl)-2-phenylethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide C26 H22 Cl2 N6 O KSIMBQNDIBGKTO-IBGZPJMESA-N
NHE	E [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4M1	Ki:  3.5999999046325684   nM  Binding MOAD
4M1	IC50:  3.640000104904175   nM  BindingDB
4M1	Ki:  3.5999999046325684   nM  BindingDB
4M1	Ki:  15   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.174 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.452	α = 90
b = 99.452	β = 90
c = 94.737	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
BUSTER	refinement
Coot	model building
AutoPROC	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-13 
• Released Date: 2015-06-03 
Deposition Author(s): Hruza, A., Reichert, P.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description