6AJI

Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with Rimonabant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of Membrane Transporter MmpL3, an Anti-TB Drug Target.

Zhang, B.Li, J.Yang, X.Wu, L.Zhang, J.Yang, Y.Zhao, Y.Zhang, L.Yang, X.Yang, X.Cheng, X.Liu, Z.Jiang, B.Jiang, H.Guddat, L.W.Yang, H.Rao, Z.

(2019) Cell 176: 636-648.e13

  • DOI: 10.1016/j.cell.2019.01.003
  • Primary Citation of Related Structures:  
    6AJF, 6AJG, 6AJH, 6AJI, 6AJJ

  • PubMed Abstract: 
  • Despite intensive efforts to discover highly effective treatments to eradicate tuberculosis (TB), it remains as a major threat to global human health. For this reason, new TB drugs directed toward new targets are highly coveted. MmpLs (Mycobacterial membrane proteins Large), which play crucial roles in transporting lipids, polymers and immunomodulators and which also extrude therapeutic drugs, are among the most important therapeutic drug targets to emerge in recent times ...

    Despite intensive efforts to discover highly effective treatments to eradicate tuberculosis (TB), it remains as a major threat to global human health. For this reason, new TB drugs directed toward new targets are highly coveted. MmpLs (Mycobacterial membrane proteins Large), which play crucial roles in transporting lipids, polymers and immunomodulators and which also extrude therapeutic drugs, are among the most important therapeutic drug targets to emerge in recent times. Here, crystal structures of mycobacterial MmpL3 alone and in complex with four TB drug candidates, including SQ109 (in Phase 2b-3 clinical trials), are reported. MmpL3 consists of a periplasmic pore domain and a twelve-helix transmembrane domain. Two Asp-Tyr pairs centrally located in this domain appear to be key facilitators of proton-translocation. SQ109, AU1235, ICA38, and rimonabant bind inside the transmembrane region and disrupt these Asp-Tyr pairs. This structural data will greatly advance the development of MmpL3 inhibitors as new TB drugs.


    Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Laboratory of Structural Biology, Tsinghua University, Beijing, 100084, China. Electronic address: raozh@mail.tsinghua.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Drug exporters of the RND superfamily-like protein,EndolysinA943Mycolicibacterium smegmatis MC2 155Escherichia virus T4
This entity is chimeric
Mutation(s): 2 
Gene Names: mmpL3MSMEI_0243eT4Tp126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt
Find proteins for A0QP27 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QP27 
Go to UniProtKB:  A0QP27
Find proteins for D9IEF7 (Enterobacteria phage T4)
Explore D9IEF7 
Go to UniProtKB:  D9IEF7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L6T (Subject of Investigation/LOI)
Query on L6T

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside
C24 H46 O11
HIJNTEBBIQHGEK-FXPCSOOLSA-N
 Ligand Interaction
AY6 (Subject of Investigation/LOI)
Query on AY6

Download Ideal Coordinates CCD File 
B [auth A]5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-N-(piperidin-1-yl)-1H-pyrazole-3-carboxamide
C22 H21 Cl3 N4 O
JZCPYUJPEARBJL-UHFFFAOYSA-N
 Ligand Interaction
MHA (Subject of Investigation/LOI)
Query on MHA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A](CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.696α = 90
b = 140.598β = 90
c = 141.833γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFC0840300
Chinese Academy of SciencesChinaXDB08020200
Ministry of Science and Technology (China)China2014CB542800
Ministry of Science and Technology (China)China2014CBA02003
National Science Foundation (China)China813300237
National Science Foundation (China)China31500607
National Science Foundation (China)China81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references