4UVG | pdb_00004uvg

Discovery of pyrimidine isoxazoles InhA in complex with compound 15

• PDB DOI: https://doi.org/10.2210/pdb4UVG/pdb

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


• Deposited: 2014-08-05 Released: 2015-09-30 
• Deposition Author(s): Read, J.A., Gingell, H., Madhavapeddi, P., Ghorpade, S., Cowan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Hitting the Target in More Than One Way: Novel, Direct Inhibitors of Mycobacterium Tuberculosis Enoyl Acp Reductase

Madhavapeddi, P., Kale, R.R., Cowen, S.D., Ghorpade, S.R., Davies, G., Bellale, E.V., Kale, M.G., Srivastava, A., Spadola, L., Kawatkar, A., Raichurkar, A.V., Tonge, M., Nandishaiah, R., Guptha, S., Narayan, A., Gingell, H., Plant, D., Landge, S., Menasinakai, S., Prabhakar, K.R., Achar, V., Ambady, A., Sambandamurthy, V.K., Ramachandran, V., Panduga, V., Reddy, J., Kumar, C.N.N., Kaur, P., Shandil, R., Iyer, P.S., Narayanan, S., Read, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 29.75 kDa 
• Atom Count: 2,377 
• Modeled Residue Count: 268 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]	A	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1  Go to UniProtKB:  P9WGR1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
A0C	E [auth A]	5-[(4,6-dimethylpyrimidin-2-yl)sulfanylmethyl]isoxazole-3-carboxamide C11 H12 N4 O2 S LDIXARLLVUNHKY-UHFFFAOYSA-N
1PE	D [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.229	α = 90
b = 96.229	β = 90
c = 139.841	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Read, J.A., Gingell, H., Madhavapeddi, P., Ghorpade, S., Cowan, S.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description