5ZJD

Lactate dehydrogenase with NADH and MLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Machilin A Inhibits Tumor Growth and Macrophage M2 Polarization Through the Reduction of Lactic Acid.

Chung, T.-W.Kim, E.-Y.Han, C.W.Park, S.Y.Jeong, M.S.Yoon, D.Choi, H.-J.Jin, L.Park, M.-J.Kwon, Y.J.Lee, H.Kim, K.-J.Park, K.H.Kim, S.Jang, S.B.Ha, K.-T.

(2019) Cancers (Basel) 11

  • DOI: 10.3390/cancers11070963
  • Primary Citation of Related Structures:  
    5ZJD, 5ZJF, 5ZJE

  • PubMed Abstract: 
  • Lactate dehydrogenase A (LDHA) is an important enzyme responsible for cancer growth and energy metabolism in various cancers via the aerobic glycolytic pathway. Here, we report that machilin A (MA), which acts as a competitive inhibitor by blocking t ...

    Lactate dehydrogenase A (LDHA) is an important enzyme responsible for cancer growth and energy metabolism in various cancers via the aerobic glycolytic pathway. Here, we report that machilin A (MA), which acts as a competitive inhibitor by blocking the nicotinamide adenine dinucleotide (NAD) binding site of LDHA, suppresses growth of cancer cells and lactate production in various cancer cell types, including colon, breast, lung, and liver cancers. Furthermore, MA markedly decreased LDHA activity, lactate production, and intracellular adenosine triphosphate (ATP) levels induced by hypoxia-induced LDHA expression in cancer cells, and significantly inhibited colony formation, leading to reduced cancer cell survival. In mouse models inoculated with murine Lewis lung carcinoma, MA significantly suppressed tumor growth as observed by a reduction of tumor volume and weight; resulting from the inhibition of LDHA activity. Subsequently, the suppression of tumor-derived lactic acid in MA-treated cancer cells resulted in decrease of neovascularization through the regulation of alternatively activated macrophages (M2) polarization in macrophages. Taken together, we suggest that the reduction of lactate by MA in cancer cells directly results in a suppression of cancer cell growth. Furthermore, macrophage polarization and activation of endothelial cells for angiogenesis were indirectly regulated preventing lactate production in MA-treated cancer cells.


    Organizational Affiliation

    Graduate Training Program of Korean Medicine for Healthy-aging, Pusan National University, Yangsan, Gyeongsangnam-do 50612, Korea. hagis@pusan.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chainABCDEFGH337Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Explore P00338 
Go to UniProtKB:  P00338
NIH Common Fund Data Resources
PHAROS  P00338
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download CCD File 
A, B, C, D, E, F, G, H
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
MLI
Query on MLI

Download CCD File 
A, B, C, D, E, F, G, H
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.007α = 90
b = 265.691β = 103.17
c = 88.006γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-20 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Han, C.W., Jang, S.B.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2015R1D1A1A01059594

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references