4Z0K | pdb_00004z0k

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 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2015.04.025
  • Primary Citation 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 0.016 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.

Macromolecule Content 

  • Total Structure Weight: 33.61 kDa 
  • Atom Count: 2,652 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 297 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IX235Homo 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
GTEx:  ENSG00000101981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IX62Homo 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
GTEx:  ENSG00000101981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.165 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.946α = 90
b = 98.946β = 90
c = 94.693γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

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: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2024-10-23
    Changes: Structure summary