8GHD

The structure of h12-LOX in hexameric form bound to inhibitor ML355 and arachidonic acid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of human arachidonate 12S-lipoxygenase bound to endogenous and exogenous inhibitors.

Mobbs, J.I.Black, K.A.Tran, M.Burger, W.A.C.Venugopal, H.Holman, T.R.Holinstat, M.Thal, D.M.Glukhova, A.

(2023) Blood 142: 1233-1242

  • DOI: https://doi.org/10.1182/blood.2023020441
  • Primary Citation of Related Structures:  
    8GHB, 8GHC, 8GHD, 8GHE

  • PubMed Abstract: 

    Human 12-lipoxygenase (12-LOX) is a key enzyme involved in platelet activation, and the regulation of its activity has been targeted for the treatment of heparin-induced thrombocytopenia. Despite the clinical importance of 12-LOX, the exact mechanisms by which it affects platelet activation are not fully understood, and the lack of structural information has limited drug discovery efforts. In this study, we used single-particle cryo-electron microscopy to determine high-resolution structures (1.7-2.8 Å) of human 12-LOX. Our results showed that 12-LOX can exist in multiple oligomeric states, from monomer to hexamer, which may affect its catalytic activity and membrane association. We also identified different conformations within the 12-LOX dimer, which likely represent different time points in its catalytic cycle. Furthermore, we identified small molecules bound to 12-LOX. The active site of the 12-LOX tetramer was occupied by an endogenous 12-LOX inhibitor, a long-chain acyl coenzyme A. In addition, we found that the 12-LOX hexamer can simultaneously bind to arachidonic acid and ML355, a selective 12-LOX inhibitor that has passed a phase 1 clinical trial for the treatment of heparin-induced thrombocytopenia and received a fast-track designation by the Food and Drug Administration. Overall, our findings provide novel insights into the assembly of 12-LOX oligomers, their catalytic mechanism, and small molecule binding, paving the way for further drug development targeting the 12-LOX enzyme.


  • Organizational Affiliation

    Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyunsaturated fatty acid lipoxygenase ALOX12
A, B, C, D, E
A, B, C, D, E, F
669Homo sapiensMutation(s): 1 
Gene Names: ALOX1212LOLOG12
EC: 1.13.11 (PDB Primary Data), 1.13.11.31 (PDB Primary Data), 1.13.11.33 (PDB Primary Data), 3.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18054 (Homo sapiens)
Explore P18054 
Go to UniProtKB:  P18054
PHAROS:  P18054
GTEx:  ENSG00000108839 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18054
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZR5 (Subject of Investigation/LOI)
Query on ZR5

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
N-(1,3-benzothiazol-2-yl)-4-{[(2-hydroxy-3-methoxyphenyl)methyl]amino}benzene-1-sulfonamide
C21 H19 N3 O4 S2
OWHBVKBNNRYMIN-UHFFFAOYSA-N
ACD (Subject of Investigation/LOI)
Query on ACD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM131835

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references