6T8V

Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole

• PDB DOI: https://doi.org/10.2210/pdb6T8V/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2019-10-25 Released: 2020-03-04 
• Deposition Author(s): Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Mac Sweeney, A., Wiesmann, C., Adams, C., Mainolfi, N., Liao, S.-M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Serrano-Wu, M., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., De Erkenez, A., Yang, L., Fang, L., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Wiesmann, C., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 

Starting Model: experimental

Literature

Discovery of 4-((2S,4S)-4-Ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic Acid (LNP023), a Factor B Inhibitor Specifically Designed To Be Applicable to Treating a Diverse Array of Complement Mediated Diseases.

Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Mac Sweeney, A., Liao, S.M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Serrano-Wu, M., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., De Erkenez, A., Yang, L., Liu, F., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ostermeier, D., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Wiesmann, C., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

(2020) J Med Chem 63: 5697-5722

• PubMed: 32073845 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b01870
• Primary Citation of Related Structures:  
  6T8U, 6T8V, 6T8W


• PubMed Abstract: 
  

  The alternative pathway (AP) of the complement system is a key contributor to the pathogenesis of several human diseases including age-related macular degeneration, paroxysmal nocturnal hemoglobinuria (PNH), atypical hemolytic uremic syndrome (aHUS), and various glomerular diseases. The serine protease factor B (FB) is a key node in the AP and is integral to the formation of C3 and C5 convertase. Despite the prominent role of FB in the AP, selective orally bioavailable inhibitors, beyond our own efforts, have not been reported previously. Herein we describe in more detail our efforts to identify FB inhibitors by high-throughput screening (HTS) and leveraging insights from several X-ray cocrystal structures during optimization efforts. This work culminated in the discovery of LNP023 ( 41 ), which is currently being evaluated clinically in several diverse AP mediated indications.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States.

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: 67.25 kDa 
• Atom Count: 4,632 
• Modelled Residue Count: 562 
• 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
MVK (Subject of Investigation/LOI)	E [auth AAA], K [auth BBB]	4-[(2~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid C23 H26 N2 O2 OTSLYLLOBTYVLP-NRFANRHFSA-N
SO4	C [auth AAA], D [auth AAA], F [auth BBB], G [auth BBB], H [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth BBB], J [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.652	α = 90
b = 97.487	β = 100.465
c = 61.975	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: 2020-03-04 
Deposition Author(s): Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Mac Sweeney, A., Wiesmann, C., Adams, C., Mainolfi, N., Liao, S.-M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Serrano-Wu, M., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., De Erkenez, A., Yang, L., Fang, L., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Wiesmann, C., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary