6QSW

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1073/pnas.1820892116
  • Primary Citation of Related Structures:  
    6QSW, 6QSX, 6RAV

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor BA [auth AAA],
B [auth BBB],
C [auth CCC]
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
GTEx:  ENSG00000243649 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00751
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JGT
Query on JGT

Download Ideal Coordinates CCD File 
G [auth AAA],
L [auth BBB],
P [auth CCC]
~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine
C14 H14 Br N3
UYAOIRISFNRFCT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth AAA]
E [auth AAA]
F [auth AAA]
H [auth BBB]
I [auth BBB]
D [auth AAA],
E [auth AAA],
F [auth AAA],
H [auth BBB],
I [auth BBB],
J [auth BBB],
K [auth BBB],
M [auth CCC],
N [auth CCC],
O [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.281α = 90
b = 91.281β = 90
c = 260.221γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-09-18
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-11-20
    Changes: Structure summary
  • Version 1.4: 2020-04-08
    Changes: Database references
  • Version 1.5: 2024-01-24
    Changes: Data collection, Database references, Refinement description