3SW2

X-ray crystal structure of human FXA in complex with 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Arylsulfonamidopiperidone derivatives as a novel class of factor Xa inhibitors.

Shi, Y.O'Connor, S.P.Sitkoff, D.Zhang, J.Shi, M.Bisaha, S.N.Wang, Y.Li, C.Ruan, Z.Michael Lawrence, R.Klei, H.E.Kish, K.Liu, E.C.Seiler, S.M.Schweizer, L.Steinbacher, T.E.Schumacher, W.A.Robl, J.A.Macor, J.E.Atwal, K.S.Stein, P.D.

(2011) Bioorg.Med.Chem.Lett. 21: 7516-7521

  • DOI: 10.1016/j.bmcl.2011.06.098

  • PubMed Abstract: 
  • The design, synthesis and SAR of a novel class of valerolactam-based arylsulfonamides as potent and selective FXa inhibitors is reported. The arylsulfonamide-valerolactam scaffold was derived based on the proposed bioisosterism to the arylcyanoguanid ...

    The design, synthesis and SAR of a novel class of valerolactam-based arylsulfonamides as potent and selective FXa inhibitors is reported. The arylsulfonamide-valerolactam scaffold was derived based on the proposed bioisosterism to the arylcyanoguanidine-caprolactam core in known FXa inhibitors. The SAR study led to compound 46 as the most potent FXa inhibitor in this series, with an IC(50) of 7 nM and EC(2×PT) of 1.7 μM. The X-ray structure of compound 40 bound to FXa shows that the sulfonamide-valerolactam scaffold anchors the aryl group in the S1 and the novel acylcytisine pharmacophore in the S4 pockets.


    Organizational Affiliation

    Research and Development, Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. Michael




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
A
94Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
B
238Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FI1
Query on FI1

Download SDF File 
Download CCD File 
B
6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide
C28 H29 Cl N4 O5 S
FLGSVBQCPOVGER-VNZMSGEBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FI1Ki: 4.7 nM (100) BINDINGDB
FI1IC50: 13 nM (100) BINDINGDB
FI1IC50: 13 nM BINDINGMOAD
FI1Ki: 4.71 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.018α = 90.00
b = 72.515β = 90.00
c = 77.956γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-13 
  • Released Date: 2011-11-16 
  • Deposition Author(s): Klei, H.E.

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Database references