2P93

Factor xa in complex with the inhibitor 5-chloro-N-(2-(4-(2-oxopyridin-1(2H)-yl)benzamido)ethyl)thiophene-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.307 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ME1Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

SAR and X-ray structures of enantiopure 1,2-cis-(1R,2S)-cyclopentyldiamine and cyclohexyldiamine derivatives as inhibitors of coagulation Factor Xa

Qiao, J.X.Chang, C.-H.Cheney, D.L.Morin, P.E.Wang, G.Z.King, S.R.Wang, T.C.Rendina, A.R.Luettgen, J.M.Knabb, R.M.Wexler, R.R.Lam, P.Y.S.

(2007) Bioorg Med Chem Lett 17: 4419-4427

  • DOI: https://doi.org/10.1016/j.bmcl.2007.06.029
  • Primary Citation of Related Structures:  
    2P93, 2P94, 2P95

  • PubMed Abstract: 

    In the search of Factor Xa (FXa) inhibitors structurally different from the pyrazole-based series, we identified a viable series of enantiopure cis-(1R,2S)-cycloalkyldiamine derivatives as potent and selective inhibitors of FXa. Among them, cyclohexyldiamide 7 and cyclopentyldiamide 9 were the most potent neutral compounds, and had good anticoagulant activity comparable to the pyrazole-based analogs. Crystal structures of 7-FXa and 9-FXa illustrate binding similarities and differences between the five- and the six-membered core systems, and provide rationales for the observed SAR of P1 and linker moieties.


  • Organizational Affiliation

    Bristol-Myers Squibb Company, Research and Development, PO Box 5400, Princeton, NJ 08543-5400, USA. jennifer.qiao@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Factor Xa234Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Factor XaB [auth L]52Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ME1
Query on ME1

Download Ideal Coordinates CCD File 
C [auth A]5-CHLORO-N-(2-(4-(2-OXOPYRIDIN-1(2H)-YL)BENZAMIDO)ETHYL)THIOPHENE-2-CARBOXAMIDE
C19 H16 Cl N3 O3 S
UCKHUNHXYMAFQM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ME1 BindingDB:  2P93 Ki: 1.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.307 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.81α = 90
b = 72.41β = 90
c = 79γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ME1Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2007-07-24 
  • Deposition Author(s): Chang, C.-H.

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Advisory, Data collection, Database references, Structure summary