4LXB image
Deposition Date 2013-07-29
Release Date 2014-06-11
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4LXB
Title:
Crystal Structure Analysis of thrombin in complex with compound D58
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Hirudo medicinalis (Taxon ID: 6421)
Method Details:
Experimental Method:
Resolution:
1.61 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Prothrombin, Thrombin light chain
Gene (Uniprot):F2
Chain IDs:A (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Hirudin variant-1
Chain IDs:B (auth: I)
Chain Length:13
Number of Molecules:1
Biological Source:Hirudo medicinalis
Polymer Type:polypeptide(L)
Molecule:Prothrombin
Gene (Uniprot):F2
Chain IDs:C (auth: L)
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
TYS B TYR O-SULFO-L-TYROSINE
Primary Citation
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.
J.Med.Chem. 56 9441 9456 (2013)
PMID: 24175584 DOI: 10.1021/jm4005835

Abstact

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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Primary Citation of related structures