6X27

Lon protease proteolytic domain complexed with bortezomib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Design of Selective LONP1 Inhibitors for Probing In Vitro Biology.

Kingsley, L.J.He, X.McNeill, M.Nelson, J.Nikulin, V.Ma, Z.Lu, W.Zhou, V.W.Manuia, M.Kreusch, A.Gao, M.Y.Witmer, D.Vaillancourt, M.T.Lu, M.Greenblatt, S.Lee, C.Vashisht, A.Bender, S.Spraggon, G.Michellys, P.Y.Jia, Y.Haling, J.R.Lelais, G.

(2021) J Med Chem 64: 4857-4869

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02152
  • Primary Citation of Related Structures:  
    6WYS, 6WZV, 6X1M, 6X27

  • PubMed Abstract: 

    LONP1 is an AAA+ protease that maintains mitochondrial homeostasis by removing damaged or misfolded proteins. Elevated activity and expression of LONP1 promotes cancer cell proliferation and resistance to apoptosis-inducing reagents. Despite the importance of LONP1 in human biology and disease, very few LONP1 inhibitors have been described in the literature. Herein, we report the development of selective boronic acid-based LONP1 inhibitors using structure-based drug design as well as the first structures of human LONP1 bound to various inhibitors. Our efforts led to several nanomolar LONP1 inhibitors with little to no activity against the 20S proteasome that serve as tool compounds to investigate LONP1 biology.


  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease homolog, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
218Homo sapiensMutation(s): 0 
Gene Names: LONP1PRSS15
EC: 3.4.21.53
UniProt & NIH Common Fund Data Resources
Find proteins for P36776 (Homo sapiens)
Explore P36776 
Go to UniProtKB:  P36776
GTEx:  ENSG00000196365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36776
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BO2 (Subject of Investigation/LOI)
Query on BO2

Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth J]
DA [auth K]
EA [auth L]
M [auth A]
AA [auth I],
CA [auth J],
DA [auth K],
EA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
T [auth E],
U [auth F],
W [auth G],
Y [auth H]
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
C19 H25 B N4 O4
GXJABQQUPOEUTA-RDJZCZTQSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
BA [auth I]
N [auth A]
P [auth B]
R [auth C]
V [auth F]
BA [auth I],
N [auth A],
P [auth B],
R [auth C],
V [auth F],
Z [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
FA [auth L],
X [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.373α = 90
b = 175.373β = 90
c = 206.189γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-05-05
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description