Experimental Data Snapshot

  • Resolution: 1.26 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XIa light chain238Homo sapiensMutation(s): 1 
Gene Names: F11
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QGS (Subject of Investigation/LOI)
Query on QGS

Download Ideal Coordinates CCD File 
B [auth A]1-[(2S)-2-{3-[(3S)-3-amino-2,3-dihydro-1-benzofuran-5-yl]-5-(propan-2-yl)phenyl}-2-hydroxyethyl]-1H-indole-7-carboxylic acid
C28 H28 N2 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
QGS Binding MOAD:  6USY Ki: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.26 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.95α = 90
b = 60.91β = 90
c = 67.3γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description