5TCC

Complement Factor D inhibited with JH4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors.

Yang, C.Y.Phillips, J.G.Stuckey, J.A.Bai, L.Sun, H.Delproposto, J.Brown, W.C.Chinnaswamy, K.

(2016) ACS Med Chem Lett 7: 1092-1096

  • DOI: 10.1021/acsmedchemlett.6b00299
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aberrant activation of the complement system is associated with diseases, including paroxysmal nocturnal hemoglobinuria and age-related macular degeneration. Complement factor D is the rate-limiting enzyme for activating the alternative pathway in th ...

    Aberrant activation of the complement system is associated with diseases, including paroxysmal nocturnal hemoglobinuria and age-related macular degeneration. Complement factor D is the rate-limiting enzyme for activating the alternative pathway in the complement system. Recent development led to a class of potent amide containing pyrrolidine derived factor D inhibitors. Here, we used biochemical enzymatic and biolayer interferometry assays to demonstrate that the amide group improves the inhibitor potency by more than 80-fold. Our crystal structures revealed buried hydrogen bond interactions are important. Molecular orbital analysis from quantum chemistry calculations dissects the chemical groups participating in these interactions. Free energy calculation supports the differential contributions of the amide group to the binding affinities of these inhibitors. Cell-based hemolysis assay confirmed these compounds inhibit factor D mediated complement activation via the alternative pathway. Our study highlights the important interactions contributing to the high potency of factor D inhibitors reported recently.


    Organizational Affiliation

    Departments of Internal Medicine and Biological Chemistry and Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.,Department of Translational Hematology and Oncology Research, Taussig Cancer Institute , Cleveland Clinic, Cleveland, Ohio 44195, United States.,Departments of Internal Medicine and Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States; Departments of Internal Medicine and Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Jiansu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , Nanjing 210009, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement factor D
A, B, C, D, E, F, G
228Homo sapiensMutation(s): 0 
Gene Names: CFD (DF, PFD)
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Go to Gene View: CFD
Go to UniProtKB:  P00746
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J56
Query on J56

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
(2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide
C18 H16 Br N5 O2 S
JSZBVXMPHMCOIC-SFHVURJKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.37 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.886α = 90.00
b = 143.745β = 90.00
c = 346.166γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-14 
  • Released Date: 2016-10-19 
  • Deposition Author(s): Stuckey, J.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesP30CA046592

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence