6RAV

Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Small-molecule factor B inhibitor for the treatment of complement-mediated diseases.

Schubart, A.Anderson, K.Mainolfi, N.Sellner, H.Ehara, T.Adams, C.M.Mac Sweeney, A.Liao, S.M.Crowley, M.Littlewood-Evans, A.Sarret, S.Wieczorek, G.Perrot, L.Dubost, V.Flandre, T.Zhang, Y.Smith, R.J.H.Risitano, A.M.Karki, R.G.Zhang, C.Valeur, E.Sirockin, F.Gerhartz, B.Erbel, P.Hughes, N.Smith, T.M.Cumin, F.Argikar, U.A.Haraldsson, B.Mogi, M.Sedrani, R.Wiesmann, C.Jaffee, B.Maibaum, J.Flohr, S.Harrison, R.Eder, J.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

  • DOI: 10.1073/pnas.1820892116
  • Primary Citation of Related Structures:  
    6RAV, 6QSW, 6QSX

  • PubMed Abstract: 
  • Dysregulation of the alternative complement pathway (AP) predisposes individuals to a number of diseases including paroxysmal nocturnal hemoglobinuria, atypical hemolytic uremic syndrome, and C3 glomerulopathy. Moreover, glomerular Ig deposits can lead to complement-driven nephropathies ...

    Dysregulation of the alternative complement pathway (AP) predisposes individuals to a number of diseases including paroxysmal nocturnal hemoglobinuria, atypical hemolytic uremic syndrome, and C3 glomerulopathy. Moreover, glomerular Ig deposits can lead to complement-driven nephropathies. Here we describe the discovery of a highly potent, reversible, and selective small-molecule inhibitor of factor B, a serine protease that drives the central amplification loop of the AP. Oral administration of the inhibitor prevents KRN-induced arthritis in mice and is effective upon prophylactic and therapeutic dosing in an experimental model of membranous nephropathy in rats. In addition, inhibition of factor B prevents complement activation in sera from C3 glomerulopathy patients and the hemolysis of human PNH erythrocytes. These data demonstrate the potential therapeutic value of using a factor B inhibitor for systemic treatment of complement-mediated diseases and provide a basis for its clinical development.


    Related Citations: 
    • Small-molecule factor B inhibitor for the treatment of complement-mediated diseases.
      Schubart, A., Anderson, K., Mainolfi, N., Sellner, H., Ehara, T., Adams, C.M., Mac Sweeney, A., Liao, S.M., Crowley, M., Littlewood-Evans, A., Sarret, S., Wieczorek, G., Perrot, L., Dubost, V., Flandre, T., Zhang, Y., Smith, R.J.H., Risitano, A.M., Karki, R.G., Zhang, C., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U.A., Haraldsson, B., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.
      (2019) Proc Natl Acad Sci U S A 116: 7926

    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland; joerg.eder@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor BA [auth AAA], B [auth BBB]291Homo sapiensMutation(s): 0 
Gene Names: CFBBFBFD
EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens)
Explore P00751 
Go to UniProtKB:  P00751
PHAROS:  P00751
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JGQ
Query on JGQ

Download Ideal Coordinates CCD File 
E [auth AAA], I [auth BBB]4-[(2~{S},4~{S})-4-ethoxy-1-[(5-methoxy-7-methyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid
C25 H30 N2 O4
RENRQMCACQEWFC-UGKGYDQZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth AAA], D [auth AAA], F [auth BBB], G [auth BBB], H [auth BBB]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth BBB], K [auth BBB]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.463α = 90
b = 97.446β = 100.475
c = 61.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-09-18
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.4: 2019-10-30
    Changes: Data collection, Database references