6TD5

Target information

RCSB PDB
6TD5
Title
Leishmania tarentolae proteasome 20S subunit complexed with LXE408 and bortezomib
Method
ELECTRON MICROSCOPY
Resolution
3.2
Classification
HYDROLASE
Organism
Leishmania donovani
Protein
Proteasome subunit beta (A0A504X6A3)
Year
2020
Publication Title
Discovery and Characterization of Clinical Candidate LXE408 as a Kinetoplastid-Selective Proteasome Inhibitor for the Treatment of Leishmaniases.
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.

External Link
RCSB PDB





Ligand information

HET
BO2
Chain ID
H
HET Number
301
Molecular Formula
C19H25BN4O4
Structure
2D structure
IUPAC Name
[(1R)-3-methyl-1-[[(2S)-3-phenyl-2-(pyrazine-2-carbonylamino)propanoyl]amino]butyl]boronic acid
InChI
InChI=1S/C19H25BN4O4/c1-13(2)10-17(20(27)28)24-18(25)15(11-14-6-4-3-5-7-14)23-19(26)16-12-21-8-9-22-16/h3-9,12-13,15,17,27-28H,10-11H2,1-2H3,(H,23,26)(H,24,25)/t15-,17-/m0/s1
InChI Key
GXJABQQUPOEUTA-RDJZCZTQSA-N
Canonical SMILES
CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cnccn1)B(O)O
Bioactivity data
CI006008

Covalent Binding

Warhead
Boronic Acid
Reaction Mechanism
Boronic Acid Addition
Residue
THR : 55
Residue Chain
H
Interactions
Pharmacophore Model



Ligand information

HET
BO2
Chain ID
I
HET Number
301
Molecular Formula
C19H25BN4O4
Structure
2D structure
IUPAC Name
[(1R)-3-methyl-1-[[(2S)-3-phenyl-2-(pyrazine-2-carbonylamino)propanoyl]amino]butyl]boronic acid
InChI
InChI=1S/C19H25BN4O4/c1-13(2)10-17(20(27)28)24-18(25)15(11-14-6-4-3-5-7-14)23-19(26)16-12-21-8-9-22-16/h3-9,12-13,15,17,27-28H,10-11H2,1-2H3,(H,23,26)(H,24,25)/t15-,17-/m0/s1
InChI Key
GXJABQQUPOEUTA-RDJZCZTQSA-N
Canonical SMILES
CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cnccn1)B(O)O
Bioactivity data
CI006008

Covalent Binding

Warhead
Boronic Acid
Reaction Mechanism
Boronic Acid Addition
Residue
THR : 30
Residue Chain
I
Interactions
Pharmacophore Model



Ligand information

HET
BO2
Chain ID
L
HET Number
401
Molecular Formula
C19H25BN4O4
Structure
2D structure
IUPAC Name
[(1R)-3-methyl-1-[[(2S)-3-phenyl-2-(pyrazine-2-carbonylamino)propanoyl]amino]butyl]boronic acid
InChI
InChI=1S/C19H25BN4O4/c1-13(2)10-17(20(27)28)24-18(25)15(11-14-6-4-3-5-7-14)23-19(26)16-12-21-8-9-22-16/h3-9,12-13,15,17,27-28H,10-11H2,1-2H3,(H,23,26)(H,24,25)/t15-,17-/m0/s1
InChI Key
GXJABQQUPOEUTA-RDJZCZTQSA-N
Canonical SMILES
CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cnccn1)B(O)O
Bioactivity data
CI006008

Covalent Binding

Warhead
Boronic Acid
Reaction Mechanism
Boronic Acid Addition
Residue
THR : 100
Residue Chain
L
Interactions
Pharmacophore Model