5SCX | pdb_00005scx

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)

• PDB DOI: https://doi.org/10.2210/pdb5SCX/pdb
• Deposition Group: G_1002223 (ground state) ExploreG_1002223

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-12-20 Released: 2022-02-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)

Mayclin, S.J., Conrady, D.G., Lorimer, D.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.07 kDa 
• Atom Count: 1,645 
• Modeled Residue Count: 172 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	179	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: folA, dfrA, Rv2763c, MTV002.28c EC: 1.5.1.3
UniProt
Find proteins for P9WNX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNX1  Go to UniProtKB:  P9WNX1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
HJI (Subject of Investigation/LOI)	C [auth A]	(2R)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid C19 H24 F2 N4 O4 UXIGBQRLXSDLOT-LBPRGKRZSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.28	α = 90
b = 67.28	β = 90
c = 72.29	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	model building
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2022-03-02
  Changes: Other, Structure summary
• Version 1.2: 2024-05-22
  Changes: Data collection