6T7P

human plasmakallikrein protease domain in complex with active site directed inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


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: 10.1021/acs.jmedchem.0c00279
  • Primary Citation of Related Structures:  
    6T7P, 6TS4, 6TS6, 6TS5, 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, ...

    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, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasma kallikrein A242Homo sapiensMutation(s): 0 
Gene Names: KLKB1KLK3
EC: 3.4.21.34
Find proteins for P03952 (Homo sapiens)
Explore P03952 
Go to UniProtKB:  P03952
NIH Common Fund Data Resources
PHAROS:  P03952
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MU8
Query on MU8

Download Ideal Coordinates CCD File 
A
(2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide
C26 H24 Cl N3 O3
WXCDYJQWHUGJRV-NMNUPHIUSA-N
 Ligand Interaction
GSH
Query on GSH

Download Ideal Coordinates CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.1α = 90
b = 59.15β = 90
c = 86.72γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-10-22 
  • Released Date: 2020-07-08 
  • Deposition Author(s): Renatus, M.

Revision History 

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