4ZAE

Development of a novel class of potent and selective FIXa inhibitors

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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

  • 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 ...

    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.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA. Electronic address: ting_zhang3@merck.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
A
235Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
B
62Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE
Download SDF File 
Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
4M1
Query on 4M1
Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4M1Ki: 3.6 - 15 nM (98) BINDINGDB
4M1Ki: 3.6 nM BINDINGMOAD
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 = 99.452α = 90.00
b = 99.452β = 90.00
c = 94.737γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
Cootmodel building
AutoPROCdata scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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