2W3I | pdb_00002w3i

Crystal Structure of FXa in complex with 4,4-disubstituted pyrrolidine-1,2-dicarboxamide inhibitor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.261 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2W3I

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Exploration of 4,4-Disubstituted Pyrrolidine-1,2-Dicarboxamides as Potent, Orally Active Factor Xa Inhibitors with Extended Duration of Action.

Van Huis, C.A.Casimiro-Garcia, A.Bigge, C.F.Cody, W.L.Dudley, D.A.Filipski, K.J.Heemstra, R.J.Kohrt, J.T.Leadley, R.J.J.Narasimhan, L.S.Mcclanahan, T.Mochalkin, I.Pamment, M.Peterson, J.T.Sahasrabudhe, V.Schaum, R.P.Edmunds, J.J.

(2009) Bioorg Med Chem 17: 2501

  • DOI: https://doi.org/10.1016/j.bmc.2009.01.063
  • Primary Citation Related Structures: 
    2W3I, 2W3K

  • PubMed Abstract: 

    Aiming to improve upon previously disclosed Factor Xa inhibitors, a series of 4,4-disubstituted pyrrolidine-1,2-dicarboxamides were explored with the intent of increasing the projected human half-life versus 5 (projected human t(1/2)=6 h). A stereospecific route to compounds containing a 4-aryl-4-hydroxypyrrolidine scaffold was developed, resulting in several compounds that demonstrated an increase in the half-life as well as an increase in the in vitro potency compared to 5. Reported herein is the discovery of 26, containing a (2R,4S)-4-hydroxy-4-(2,4-difluorophenyl)-pyrrolidine scaffold, which is a selective, orally bioavailable, efficacious Factor Xa inhibitor that appears suitable for a once-daily dosing (projected human t(1/2)=23 h).


  • Organizational Affiliation
    • Michigan Laboratories, Ann Arbor Campus, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.

Macromolecule Content 

  • Total Structure Weight: 32.51 kDa 
  • Atom Count: 2,431 
  • Modeled Residue Count: 284 
  • Deposited Residue Count: 285 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COAGULATION FACTOR X, HEAVY CHAIN234Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
COAGULATION FACTOR X, LIGHT CHAIN51Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L1C

Query on L1C



Download:Ideal Coordinates CCD File
D [auth A](2R,4S)-N^1^-(4-chlorophenyl)-4-(2,4-difluorophenyl)-4-hydroxy-N^2^-(2-oxo-2H-1,3'-bipyridin-6'-yl)pyrrolidine-1,2-dicarboxamide
C28 H22 Cl F2 N5 O4
BGECSWGTDIXGJY-QDPGVEIFSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.261 (Depositor) 
  • R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.298α = 90
b = 72.688β = 90
c = 77.685γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary