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 
  • R-Value Observed: 0.149 

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
  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXA235Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXB62Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4M1
Query on 4M1

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
E [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4M1Ki:  3.5999999046325684   nM  Binding MOAD
4M1IC50:  3.640000104904175   nM  BindingDB
4M1Ki:  3.5999999046325684   nM  BindingDB
4M1Ki:  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 = 99.452α = 90
b = 99.452β = 90
c = 94.737γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BUSTERrefinement
Cootmodel building
AutoPROCdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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