6DDP | pdb_00006ddp

Mycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.225 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6DDP

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Drugging the Folate Pathway in Mycobacterium tuberculosis: The Role of Multi-targeting Agents.

Hajian, B.Scocchera, E.Shoen, C.Krucinska, J.Viswanathan, K.G-Dayanandan, N.Erlandsen, H.Estrada, A.Mikusova, K.Kordulakova, J.Cynamon, M.Wright, D.

(2019) Cell Chem Biol 26: 781-791.e6

  • DOI: https://doi.org/10.1016/j.chembiol.2019.02.013
  • Primary Citation Related Structures: 
    6DDP, 6DDS, 6DDW, 6DE4, 6DE5

  • PubMed Abstract: 

    The folate biosynthetic pathway offers many druggable targets that have yet to be exploited in tuberculosis therapy. Herein, we have identified a series of small molecules that interrupt Mycobacterium tuberculosis (Mtb) folate metabolism by dual targeting of dihydrofolate reductase (DHFR), a key enzyme in the folate pathway, and its functional analog, Rv2671. We have also compared the antifolate activity of these compounds with that of para-aminosalicylic acid (PAS). We found that the bioactive metabolite of PAS, in addition to previously reported activity against DHFR, inhibits flavin-dependent thymidylate synthase in Mtb, suggesting a multi-targeted mechanism of action for this drug. Finally, we have shown that antifolate treatment in Mtb decreases the production of mycolic acids, most likely due to perturbation of the activated methyl cycle. We conclude that multi-targeting of the folate pathway in Mtb is associated with highly potent anti-mycobacterial activity.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.

Macromolecule Content 

  • Total Structure Weight: 75.29 kDa 
  • Atom Count: 5,652 
  • Modeled Residue Count: 636 
  • Deposited Residue Count: 636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrofolate reductase
A, B, C, D
159Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: folAdfrARv2763cMTV002.28c
EC: 1.5.1.3
UniProt
Find proteins for P9WNX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNX1 
Go to UniProtKB:  P9WNX1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNX1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C],
K [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
G6Y

Query on G6Y



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
I [auth C],
L [auth D]
3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid
C24 H24 N4 O3
OKJCHFXBCVXSIZ-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.77α = 90.04
b = 60.552β = 90.02
c = 60.637γ = 90.03
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI104841

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description