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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cruzipain
A, B
215Trypanosoma cruziMutation(s): 2 
EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi)
Go to UniProtKB:  P25779
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
25B
Query on 25B

Download SDF File 
Download CCD File 
A, B
(1R,2R)-2-[(4-chlorophenyl)carbonyl]-N-{(1S)-1-[2-(phenylsulfonyl)ethyl]pentyl}cyclohexanecarboxamide
(1R,2R)-2-(4-chlorobenzoyl)-N-((S,E)-1-(phenylsulfonyl)hept-1-en-3-yl)cyclohexanecarboxamide
C27 H34 Cl N O4 S
GOPKEHWOLDXUST-ICDZXHCJSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
25BIC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.687α = 90.00
b = 72.493β = 89.79
c = 60.930γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance