4BTI

factor Xa in complex with the dual thrombin-FXa inhibitor 58.

• PDB DOI:  https://doi.org/10.2210/pdb4BTI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-18 Released: 2013-12-25 
• Deposition Author(s): Meneyrol, J., Follmann, M., Lassalle, G., Wehner, V., Barre, G., Rousseaux, T., Altenburger, J.M., Petit, F., Bocskei, Z., Stehlin-Gaon, C., Schreuder, H., Alet, N., Herault, J.-P., Millet, L., Dol, F., Hasbrand, C., Schaeffer, P., Sadoun, F., Klieber, S., Briot, C., Bono, F., Herbert, J.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

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

• PubMed: 24175584 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.55 kDa 
• Atom Count: 5,193 
• Modelled Residue Count: 578 
• Deposited Residue Count: 700 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X HEAVY CHAIN	A, C [auth E]	96	Homo sapiens	Mutation(s): 0  Gene Names: F10 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X LIGHT CHAIN	B, D [auth F]	254	Homo sapiens	Mutation(s): 0  Gene Names: F10 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7R9	F [auth B], H [auth F]	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
CA	E [auth B], G [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7R9	Binding MOAD:  4BTI	IC50: 0.2 (nM) from 1 assay(s)
	PDBBind:  4BTI	IC50: 0.2 (nM) from 1 assay(s)
	BindingDB:  4BTI	IC50: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.224 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.65	α = 90
b = 55.65	β = 90
c = 173.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Meneyrol, J., Follmann, M., Lassalle, G., Wehner, V., Barre, G., Rousseaux, T., Altenburger, J.M., Petit, F., Bocskei, Z., Stehlin-Gaon, C., Schreuder, H., Alet, N., Herault, J.-P., Millet, L., Dol, F., Hasbrand, C., Schaeffer, P., Sadoun, F., Klieber, S., Briot, C., Bono, F., Herbert, J.-M.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-01-15
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other