6TCZ

Leishmania tarentolae proteasome 20S subunit complexed with LXE408


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery and Characterization of Clinical Candidate LXE408 as a Kinetoplastid-Selective Proteasome Inhibitor for the Treatment of Leishmaniases.

Nagle, A.Biggart, A.Be, C.Srinivas, H.Hein, A.Caridha, D.Sciotti, R.J.Pybus, B.Kreishman-Deitrick, M.Bursulaya, B.Lai, Y.H.Gao, M.Y.Liang, F.Mathison, C.J.N.Liu, X.Yeh, V.Smith, J.Lerario, I.Xie, Y.Chianelli, D.Gibney, M.Berman, A.Chen, Y.L.Jiricek, J.Davis, L.C.Liu, X.Ballard, J.Khare, S.Eggimann, F.K.Luneau, A.Groessl, T.Shapiro, M.Richmond, W.Johnson, K.Rudewicz, P.J.Rao, S.P.S.Thompson, C.Tuntland, T.Spraggon, G.Glynne, R.J.Supek, F.Wiesmann, C.Molteni, V.

(2020) J Med Chem 63: 10773-10781

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00499
  • Primary Citation of Related Structures:  
    6TCZ, 6TD5

  • PubMed Abstract: 

    Visceral leishmaniasis is responsible for up to 30,000 deaths every year. Current treatments have shortcomings that include toxicity and variable efficacy across endemic regions. Previously, we reported the discovery of GNF6702, a selective inhibitor of the kinetoplastid proteasome, which cleared parasites in murine models of leishmaniasis, Chagas disease, and human African trypanosomiasis. Here, we describe the discovery and characterization of LXE408, a structurally related kinetoplastid-selective proteasome inhibitor currently in Phase 1 human clinical trials. Furthermore, we present high-resolution cryo-EM structures of the Leishmania tarentolae proteasome in complex with LXE408, which provides a compelling explanation for the noncompetitive mode of binding of this novel class of inhibitors of the kinetoplastid proteasome.


  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation (GNF), San Diego, California 92121, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeA,
O [auth a]
250Leishmania donovaniMutation(s): 0 
Gene Names: PaCGC20_14335CGC21_7870LdCL_350054100
EC: 3.4.25.1
UniProt
Find proteins for Q9UAB4 (Leishmania donovani)
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UniProt GroupQ9UAB4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB,
P [auth b]
231Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_21935CGC21_34645LdCL_210026400
EC: 3.4.25.1
UniProt
Find proteins for A0A3Q8IB07 (Leishmania donovani)
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UniProt GroupA0A3Q8IB07
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC,
Q [auth c]
285Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_4565LdCL_140008100
EC: 3.4.25.1
UniProt
Find proteins for A0A504Y5E1 (Leishmania donovani)
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UniProt GroupA0A504Y5E1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexD,
R [auth d]
248Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_1080
EC: 3.4.25.1
UniProt
Find proteins for A0A504XWY9 (Leishmania donovani)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE,
S [auth e]
344Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_21875CGC21_34705LdCL_210027700
EC: 3.4.25.1
UniProt
Find proteins for A0A3Q8IC41 (Leishmania donovani)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeF,
T [auth f]
428Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_29090CGC21_13150
EC: 3.4.25.1
UniProt
Find proteins for A0A504XQ80 (Leishmania donovani)
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UniProt GroupA0A504XQ80
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexG,
U [auth g]
238Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_1425CGC20_33255CGC21_31345LdCL_270006800
EC: 3.4.25.1
UniProt
Find proteins for A0A3S5H7H2 (Leishmania donovani)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaH,
V [auth h]
283Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_24015CGC21_10040
EC: 3.4.25.1
UniProt
Find proteins for A0A504X6A3 (Leishmania donovani)
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UniProt GroupA0A504X6A3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaI,
W [auth i]
254Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_14810CGC21_7390LdCL_350043900
EC: 3.4.25.1
UniProt
Find proteins for A0A3Q8IVH0 (Leishmania donovani)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaJ,
X [auth j]
205Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_14015CGC21_21605LdCL_280006000
EC: 3.4.25.1
UniProt
Find proteins for A0A3S7X127 (Leishmania donovani)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit family proteinK,
Y [auth k]
206Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_12505
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaL,
Z [auth l]
302Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_29060CGC21_13180LdCL_360022800
EC: 3.4.25.1
UniProt
Find proteins for A0A3Q8IIY4 (Leishmania donovani)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth m],
M
339Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_20280CGC21_24485LdCL_060006300
EC: 3.4.25.1
UniProt
Find proteins for A0A3S7WPD8 (Leishmania donovani)
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UniProt GroupA0A3S7WPD8
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth n],
N
220Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_27345CGC21_27360LdCL_340051000LdCL_340051300
EC: 3.4.25.1
UniProt
Find proteins for A0A3Q8IIL6 (Leishmania donovani)
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UniProt GroupA0A3Q8IIL6
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N2E (Subject of Investigation/LOI)
Query on N2E

Download Ideal Coordinates CCD File 
CA [auth L],
DA [auth l]
~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl]phenyl]-2,4-dimethyl-1,3-oxazole-5-carboxamide
C23 H18 F N7 O2
GNVVPYCWVLCWKV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2020-08-26 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references