4LXB

Crystal Structure Analysis of thrombin in complex with compound D58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.M.Petit, F.Bocskei, Z.Schreuder, H.Alet, N.Herault, J.P.Millet, L.Dol, F.Florian, P.Schaeffer, P.Sadoun, F.Klieber, S.Briot, C.Bono, F.Herbert, J.M.

(2013) J.Med.Chem. 56: 9441-9456

  • DOI: 10.1021/jm4005835
  • Primary Citation of Related Structures:  

  • 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, resp ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin, Thrombin light chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-1
I
13Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
Go to UniProtKB:  P01050
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
7R9
Query on 7R9

Download SDF File 
Download CCD File 
H
5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide
C26 H32 Cl F2 N5 O6 S2
GMYAFDWQODYJNI-IRXDYDNUSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7R9IC50: 7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.623α = 90.00
b = 71.274β = 100.84
c = 72.858γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
AMoREphasing
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release