4Z0K

Rapid development of two Factor IXa inhibitors from Hit to Lead


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rapid development of two factor IXa inhibitors from hit to lead.

Parker, D.L.Walsh, S.Li, B.Kim, E.Sharipour, A.Smith, C.Chen, Y.H.Berger, R.Harper, B.Zhang, T.Park, M.Shu, M.Wu, J.Xu, J.Dewnani, S.Sherer, E.C.Hruza, A.Reichert, P.Geissler, W.Sonatore, L.Ellsworth, K.Balkovec, J.Greenlee, W.Wood, H.B.

(2015) Bioorg.Med.Chem.Lett. 25: 2321-2325

  • DOI: 10.1016/j.bmcl.2015.04.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two high-throughput screening hits were investigated for SAR against human factor IXa. Both hits feature a benzamide linked to a [6-5]-heteroaryl via an alkyl amine. In the case where this system is a benzimidazolyl-ethyl amine the binding potency fo ...

    Two high-throughput screening hits were investigated for SAR against human factor IXa. Both hits feature a benzamide linked to a [6-5]-heteroaryl via an alkyl amine. In the case where this system is a benzimidazolyl-ethyl amine the binding potency for the hit was improved >500-fold, from 9 μM to 0.016 μM. For the other hit, which contains a tetrahydropyrido-indazole amine, potency was improved 20-fold, from 2 μM to 0.09 μM. X-ray crystal structures were obtained for an example of each class which improved understanding of the binding, and will enable further drug discovery efforts.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck and Co., Inc, PO Box 2000, E. Lincoln Ave., Rahway, NJ 07016, USA. Electronic address: dann_parker@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 4 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
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NHE
Query on NHE

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Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
4LN
Query on 4LN

Download SDF File 
Download CCD File 
A
N-[(2R)-10-hydroxy-2,7-dimethyl-1,2,3,4-tetrahydropyrido[1,2-b]indazol-2-yl]-4-(4H-1,2,4-triazol-4-yl)benzamide
C22 H22 N6 O2
GHULVZIKWFGNRE-JOCHJYFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.147 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 98.946α = 90.00
b = 98.946β = 90.00
c = 94.693γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release