6HHQ

Crystal structure of compound C45 bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.

Pellegrino, S.Meyer, M.Konst, Z.A.Holm, M.Voora, V.K.Kashinskaya, D.Zanette, C.Mobley, D.L.Yusupova, G.Vanderwal, C.D.Blanchard, S.C.Yusupov, M.

(2019) Nucleic Acids Res 47: 3223-3232

  • DOI: 10.1093/nar/gkz053
  • Primary Citation of Related Structures:  
    6HHQ

  • PubMed Abstract: 
  • Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity ...

    Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity. Toward this goal, we have previously established a short synthesis pathway that grants access to multiple congeners of the lissoclimide family. Here we present the X-ray co-crystal structure at 3.1 Å resolution of C45, a potent congener with two A-ring chlorine-bearing stereogenic centers with 'unnatural' configurations, with the yeast 80S ribosome, intermolecular interaction energies of the C45/ribosome complex, and single-molecule FRET data quantifying the impact of C45 on both human and yeast ribosomes. Together, these data provide new insights into the role of unusual non-covalent halogen bonding interactions involved in the binding of this synthetic compound to the 80S ribosome.


    Organizational Affiliation

    Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.



Macromolecules

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Entity ID: 4
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60S ribosomal protein L2-A CDj254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 CEk387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A CFl362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 CGm297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-A CHn176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A CIo244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A CJp256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A CKq191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 CLr221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-B CMs174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-A CNt199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A COu138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A CPv204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A CQw199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A CRx184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A CSy186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A CTz189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A 0CU172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A 2CV160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A 5CW121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A 6CX137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A 7CY155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 8CZ142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A 9DA127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A AADB136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 ABDC149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 ACDD59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30 ADDE105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-A AEDF113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32 AFDG130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-A AGDH107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-A AHDI121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-A AIDJ120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-A AJDK100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-A AKDL88Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38 ALDM78Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39 AMDN51Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40 ANDO128Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-B AODP25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-A APDQ106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-A AQDR92Saccharomyces cerevisiaeMutation(s): 0 
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Suppressor protein STM1 isM273Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein P0 p0312Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-A Bs0252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-A Cs1255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 Ds2254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 Es3240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-A Fs4261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5 Gs5225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-A Hs6236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-A Is7190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-A Js8200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-A Ks9197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-A Lc0105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-A Mc1156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 Nc2143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 Oc3151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-B Pc4138Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 Qc5142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A Rc6143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-A Sc7136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A Tc8146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-A Uc9144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S20 Vd0121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S21-A Wd187Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S22-A Xd2130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S23-A Yd3145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S24-A Zd4135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S25-A ad5108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S26-B bd6119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S27-A cd782Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S28-A dd867Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S29-A d9e56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S30-A e0f63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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Ubiquitin-40S ribosomal protein S31 e1g152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Guanine nucleotide-binding protein subunit beta-like protein Rbh319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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25S ribosomal RNA1, AR3396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNA3, AS121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNA4, AT158Saccharomyces cerevisiae
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Entity ID: 47
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18S ribosomal RNAA1797Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChainsLengthOrganismImage
18S ribosomal RNAsR1800Saccharomyces cerevisiae
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G5B
Query on G5B

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1, AR
(3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione
C20 H29 Cl2 N O3
PPKXULKLJJFMKB-RHKPTJIRSA-N
 Ligand Interaction
OHX
Query on OHX

Download Ideal Coordinates CCD File