6TS4

Coagulation factor XI protease domain in complex with active site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach.

Lorthiois, E.Roache, J.Barnes-Seeman, D.Altmann, E.Hassiepen, U.Turner, G.Duvadie, R.Hornak, V.Karki, R.G.Schiering, N.Weihofen, W.A.Perruccio, F.Calhoun, A.Fazal, T.Dedic, D.Durand, C.Dussauge, S.Fettis, K.Tritsch, F.Dentel, C.Druet, A.Liu, D.Kirman, L.Lachal, J.Namoto, K.Bevan, D.Mo, R.Monnet, G.Muller, L.Zessis, R.Huang, X.Lindsley, L.Currie, T.Chiu, Y.H.Fridrich, C.Delgado, P.Wang, S.Hollis-Symynkywicz, M.Berghausen, J.Williams, E.Liu, H.Liang, G.Kim, H.Hoffmann, P.Hein, A.Ramage, P.D'Arcy, A.Harlfinger, S.Renatus, M.Ruedisser, S.Feldman, D.Elliott, J.Sedrani, R.Maibaum, J.Adams, C.M.

(2020) J Med Chem 63: 8088-8113

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00279
  • Primary Citation of Related Structures:  
    6T7P, 6TS4, 6TS5, 6TS6, 6TS7, 6USY

  • PubMed Abstract: 

    The serine protease factor XI (FXI) is a prominent drug target as it holds promise to deliver efficacious anticoagulation without an enhanced risk of major bleeds. Several efforts have been described targeting the active form of the enzyme, FXIa. Herein, we disclose our efforts to identify potent, selective, and orally bioavailable inhibitors of FXIa. Compound 1 , identified from a diverse library of internal serine protease inhibitors, was originally designed as a complement factor D inhibitor and exhibited submicromolar FXIa activity and an encouraging absorption, distribution, metabolism, and excretion (ADME) profile while being devoid of a peptidomimetic architecture. Optimization of interactions in the S1, S1β, and S1' pockets of FXIa through a combination of structure-based drug design and traditional medicinal chemistry led to the discovery of compound 23 with subnanomolar potency on FXIa, enhanced selectivity over other coagulation proteases, and a preclinical pharmacokinetics (PK) profile consistent with bid dosing in patients.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XI238Homo sapiensMutation(s): 2 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
GTEx:  ENSG00000088926 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J7B (Subject of Investigation/LOI)
Query on J7B

Download Ideal Coordinates CCD File 
K [auth A]2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid
C22 H20 N2 O3
VEQODTWEXCBUAZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J7B Binding MOAD:  6TS4 IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.32α = 90
b = 60.8β = 90
c = 66.87γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references, Derived calculations