6QSX

Complement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.220 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JGNClick on this verticalbar to view details

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]
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JGN
Query on JGN

Download Ideal Coordinates CCD File 
F [auth AAA],
K [auth BBB]
[(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol
C18 H26 N2 O2
MBNDMTBONUNJAQ-GJZGRUSLSA-N
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
L [auth BBB],
M [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JGN BindingDB:  6QSX IC50: 3350 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.592α = 90
b = 98.06β = 99.174
c = 61.721γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JGNClick on this verticalbar to view details

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, Structure summary
  • Version 1.2: 2019-09-18
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary