3HD3

High resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor SMDC-256047


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases.

Bryant, C.Kerr, I.D.Debnath, M.Ang, K.K.Ratnam, J.Ferreira, R.S.Jaishankar, P.Zhao, D.Arkin, M.R.McKerrow, J.H.Brinen, L.S.Renslo, A.R.

(2009) Bioorg Med Chem Lett 19: 6218-6221

  • DOI: 10.1016/j.bmcl.2009.08.098
  • Primary Citation of Related Structures:  
    3HD3

  • PubMed Abstract: 
  • We describe here the identification of non-peptidic vinylsulfones that inhibit parasite cysteine proteases in vitro and inhibit the growth of Trypanosoma brucei brucei parasites in culture. A high resolution (1.75 A) co-crystal structure of 8a bound to cruzain reveals how the non-peptidic P2/P3 moiety in such analogs bind the S2 and S3 subsites of the protease, effectively recapitulating important binding interactions present in more traditional peptide-based protease inhibitors and natural substrates ...

    We describe here the identification of non-peptidic vinylsulfones that inhibit parasite cysteine proteases in vitro and inhibit the growth of Trypanosoma brucei brucei parasites in culture. A high resolution (1.75 A) co-crystal structure of 8a bound to cruzain reveals how the non-peptidic P2/P3 moiety in such analogs bind the S2 and S3 subsites of the protease, effectively recapitulating important binding interactions present in more traditional peptide-based protease inhibitors and natural substrates.


    Organizational Affiliation

    Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CruzipainA, B215Trypanosoma cruziMutation(s): 2 
Gene Names: cruzain
EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi)
Explore P25779 
Go to UniProtKB:  P25779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
25B
Query on 25B

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
(1R,2R)-2-[(4-chlorophenyl)carbonyl]-N-{(1S)-1-[2-(phenylsulfonyl)ethyl]pentyl}cyclohexanecarboxamide
C27 H34 Cl N O4 S
GOPKEHWOLDXUST-ICDZXHCJSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download Ideal Coordinates CCD File 
E [auth A]ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
25B PDBBind:  3HD3 IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.687α = 90
b = 72.493β = 89.79
c = 60.93γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations