Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 33682.19 
• Atom Count: 2307 
• 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): 1 


• 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 

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


• 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. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor IX	A	235	Homo sapiens	Mutation(s): 1  Gene Names: F9 EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens) Go to Gene View: F9 Go to UniProtKB:  P00740

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor IX	B	62	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens) Go to Gene View: F9 Go to UniProtKB:  P00740

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NHE	A	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID N-CYCLOHEXYLTAURINE; CHES C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
4M1	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4M1	Ki: 3.6 - 15 nM (98) BINDINGDB

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 99.452	α = 90.00
b = 99.452	β = 90.00
c = 94.737	γ = 120.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Database references, Derived calculations, Refinement description