5EGM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.841 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2015.07.078

  • 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) s ...

    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.


    Organizational Affiliation

    Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA. Electronic address: dongfang-meng@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
5NY
Query on 5NY

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Download CCD File 
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
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.841 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 99.298α = 90.00
b = 99.298β = 90.00
c = 94.685γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
BUSTERrefinement
AutoPROCdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description