4YZU

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: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    4YZU, 4Z0K

  • 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 for the hit was improved >500-fold, from 9 μM to 0 ...

    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.



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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4K6 (Subject of Investigation/LOI)
Query on 4K6

Download Ideal Coordinates CCD File 
C [auth A]N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide
C20 H20 N6 O
QNOXZLGNUKPKFJ-UHFFFAOYSA-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
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4K6 BindingDB:  4YZU Ki: 9000 (nM) from 1 assay(s)
Binding MOAD:  4YZU Ki: 9000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.911α = 90
b = 98.911β = 90
c = 94.61γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy