4BTT

factor Xa in complex with the dual thrombin-FXa inhibitor 31.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

5-Chlorothiophene-2-Carboxylic Acid [(S)-2-[2-Methyl-3-(2-Oxopyrrolidin-1-Yl)Benzenesulfonylamino]-3-(4-Methylpiperazin-1-Yl)-3-Oxopropyl]Amide (Sar107375), a Selective and Potent Orally Active Dual Thrombin and Factor Xa Inhibitor.

Meneyrol, J.Follmann, M.Lassalle, G.Wehner, V.Barre, G.Rousseaux, T.Altenburger, J.Petit, F.Bocskei, Z.Schreuder, H.Alet, N.Herault, J.Millet, L.Dol, F.Florian, P.Schaeffer, P.Sadoun, F.Klieber, S.Briot, C.Bono, F.Herbert, J.

(2013) J Med Chem 56: 9441

  • DOI: https://doi.org/10.1021/jm4005835
  • Primary Citation of Related Structures:  
    4BTI, 4BTT, 4BTU, 4LOY, 4LXB

  • PubMed Abstract: 

    Compound 15 (SAR107375), a novel potent dual thrombin and factor Xa inhibitor resulted from a rational optimization process. Starting from compound 14, with low factor Xa and modest anti-thrombin inhibitory activities (IC50's of 3.5 and 0.39 μM, respectively), both activities were considerably improved, notably through the incorporation of a neutral chlorothiophene P1 fragment and tuning of P2 and P3-P4 fragments. Final optimization of metabolic stability with microsomes led to the identification of 15, which displays strong activity in vitro vs factor Xa and thrombin (with Ki's of 1 and 8 nM, respectively). In addition 15 presents good selectivity versus related serine proteases (roughly 300-fold), including trypsin (1000-fold), and is very active (0.39 μM) in the thrombin generation time (TGT) coagulation assay in human platelet rich plasma (PRP). Potent in vivo activity in a rat model of venous thrombosis following iv and, more importantly, po administration was also observed (ED50 of 0.07 and 2.8 mg/kg, respectively). Bleeding liability was reduced in the rat wire coil model, more relevant to arterial thrombosis, with 15 (blood loss increase of 2-fold relative to the ED80 value) compared to rivaroxaban 2 and dabigatran etexilate 1a.


  • Organizational Affiliation

    Sanofi-Aventis R&D , 195 Route d'Espagne, 31036 Toulouse Cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COAGULATION FACTOR X LIGHT CHAINA,
C [auth E]
96Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COAGULATION FACTOR XB,
D [auth F]
254Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VYR
Query on VYR

Download Ideal Coordinates CCD File 
F [auth B],
H [auth F]
N-[(S)-1-[5-(5-Chloro-thiophen-2-yl)-isoxazol-3-ylmethyl]-2-(4-methoxy-piperidin-1-yl)-2-oxo-ethyl]-2-ethyl-3-(3-oxo-morpholin-4-yl)-benzenesulfonamide
C28 H33 Cl N4 O7 S2
VOALXMVXTCHJGT-NRFANRHFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth B],
G [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VYR PDBBind:  4BTT IC50: 1.43 (nM) from 1 assay(s)
BindingDB:  4BTT IC50: 2.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.21α = 90
b = 56.21β = 90
c = 175.44γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary