6EX8

Crystal Structure of Rhodesain in complex with a Macrolactam Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

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Literature

Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors.

Giroud, M.Dietzel, U.Anselm, L.Banner, D.Kuglstatter, A.Benz, J.Blanc, J.B.Gaufreteau, D.Liu, H.Lin, X.Stich, A.Kuhn, B.Schuler, F.Kaiser, M.Brun, R.Schirmeister, T.Kisker, C.Diederich, F.Haap, W.

(2018) J Med Chem 61: 3350-3369

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01869
  • Primary Citation of Related Structures:  
    6EX8, 6EXO, 6EXQ, 6EZP, 6EZX, 6F06

  • PubMed Abstract: 

    Rhodesain (RD) is a parasitic, human cathepsin L (hCatL) like cysteine protease produced by Trypanosoma brucei ( T. b.) species and a potential drug target for the treatment of human African trypanosomiasis (HAT). A library of hCatL inhibitors was screened, and macrocyclic lactams were identified as potent RD inhibitors ( K i < 10 nM), preventing the cell-growth of Trypanosoma brucei rhodesiense (IC 50 < 400 nM). SARs addressing the S2 and S3 pockets of RD were established. Three cocrystal structures with RD revealed a noncovalent binding mode of this ligand class due to oxidation of the catalytic Cys25 to a sulfenic acid (Cys-SOH) during crystallization. The P-glycoprotein efflux ratio was measured and the in vivo brain penetration in rats determined. When tested in vivo in acute HAT model, the compounds permitted up to 16.25 (vs 13.0 for untreated controls) mean days of survival.


  • Organizational Affiliation

    Department of Tropical Medicine , Medical Mission Institute , Salvatorstrasse 7 , 97074 Würzburg , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine protease
A, B
217Trypanosoma brucei rhodesienseMutation(s): 1 
Gene Names: rhodesain
UniProt
Find proteins for Q95PM0 (Trypanosoma brucei rhodesiense)
Explore Q95PM0 
Go to UniProtKB:  Q95PM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95PM0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2K
Query on C2K

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
(3~{S})-~{N}-[1-(aminomethyl)cyclopropyl]-19-chloranyl-5-oxidanylidene-9-(trifluoromethyl)-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(20),6(11),7,9,18,21-hexaene-3-carboxamide
C25 H27 Cl F3 N3 O4
BNWIQPLOOOQIPB-IBGZPJMESA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
C2K Binding MOAD:  6EX8 Ki: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.83α = 103.56
b = 49.753β = 98.89
c = 67.569γ = 100.81
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 630

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description