6QSX | pdb_00006qsx

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.

• PDB DOI: https://doi.org/10.2210/pdb6QSX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Drosophila sp. (in: flies)
• Mutation(s): No 


• Deposited: 2019-02-22 Released: 2019-03-27 
• Deposition Author(s): Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 

Starting Model: experimental

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

• PubMed: 30926668 
• DOI: https://doi.org/10.1073/pnas.1820892116
• Primary Citation 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.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland.
Novartis Institutes for BioMedical Research, Cambridge, MA 02139.
Ophthalmology, Biogen, Cambridge, MA 02142.
Kymera Therapeutics, Cambridge, MA 02139.
PeptiDream Inc., Kawasaki-shi, 210-0821 Kanagawa, Japan.
Drug Discovery Biology, Idorsia Pharmaceuticals Ltd., 4123 Allschwil, Switzerland.
Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242.
Department of Clinical Medicine and Surgery, Bone Marrow Transplantation Program, Federico II University, 80138 Naples, Italy.
Medicinal Chemistry, Cardiovascular, Renal & Metabolism, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 431 83 Mölndal, Sweden.
Protein Sciences, Abcam PLC, CB4 0GZ Cambridge, United Kingdom.
Institute of Infection and Immunity, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom.
Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.32 kDa 
• Atom Count: 4,940 
• Modeled Residue Count: 571 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor B	A [auth AAA], B [auth BBB]	291	Homo sapiens	Mutation(s): 0  Gene Names: CFB, BF, BFD 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JGN	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	C [auth AAA], D [auth AAA], E [auth AAA], G [auth BBB], H [auth BBB], I [auth BBB], J [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	L [auth BBB], M [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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), 0.219 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.592	α = 90
b = 98.06	β = 99.174
c = 61.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

Revision History  

• 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