4IV6

X-ray crystal structure of an isovaleryl-CoA dehydrogenase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Increasing the structural coverage of tuberculosis drug targets.

Baugh, L.Phan, I.Begley, D.W.Clifton, M.C.Armour, B.Dranow, D.M.Taylor, B.M.Muruthi, M.M.Abendroth, J.Fairman, J.W.Fox, D.Dieterich, S.H.Staker, B.L.Gardberg, A.S.Choi, R.Hewitt, S.N.Napuli, A.J.Myers, J.Barrett, L.K.Zhang, Y.Ferrell, M.Mundt, E.Thompkins, K.Tran, N.Lyons-Abbott, S.Abramov, A.Sekar, A.Serbzhinskiy, D.Lorimer, D.Buchko, G.W.Stacy, R.Stewart, L.J.Edwards, T.E.Van Voorhis, W.C.Myler, P.J.

(2015) Tuberculosis (Edinb) 95: 142-148

  • DOI: 10.1016/j.tube.2014.12.003
  • Primary Citation of Related Structures:  
    3P0T, 3P2Y, 3P4T, 3P4I, 3P5M, 3P85, 3PE8, 3PK0, 3PPI, 3Q1T, 3QIV, 3QKA, 3QK8, 3QLJ, 3QMJ, 3R0O, 3R1J, 3R20, 3R1I, 3R2N, 3QRE, 3R4T, 3Q8N, 3PZY, 3QBP, 3QDF, 3QHA, 4GK6, 4HDT, 3MYB, 3NDN, 3NDO, 3NF4, 3NG3, 3NJD, 3O0M, 3OI9, 3O38, 3NWO, 3OC7, 3OC6, 3OKS, 3OME, 3KHP, 3UVE, 3UCX, 4DI1, 4DIE, 4DQ8, 3HWK

  • PubMed Abstract: 
  • High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites ...

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States. Electronic address: peter.myler@seattlebiomed.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenase FadE3A, B388Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: fadE3MSMEI_1947MSMEG_1991
EC: 1.3.8.1
UniProt
Find proteins for A0QTW7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QTW7 
Go to UniProtKB:  A0QTW7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA (Subject of Investigation/LOI)
Query on FDA

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.82α = 90
b = 105.82β = 90
c = 169.49γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references