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Structure paper

TitleUsing a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis.
Journal, issue, pagesAcs Infect Dis., Vol. 6, Page 2192-2201, Year 2020
Publish dateFeb 10, 2020 (structure data deposition date)
AuthorsRibeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. ...Ribeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. / Parise-Filho, R. / Coyne, A.G. / Blundell, T.L. / Abell, C. / Dias, M.V.B.
External linksAcs Infect Dis. / PubMed:32603583
MethodsX-ray diffraction
Resolution1.45 - 2.683 Å
Structure data

PDB-6vs5:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 5-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid (fragment 1)
Method: X-RAY DIFFRACTION / Resolution: 1.758 Å

PDB-6vs6:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(furan-2-yl)-1-methyl-1H-pyrazole-5-carboxylic acid (fragment 2)
Method: X-RAY DIFFRACTION / Resolution: 1.853 Å

PDB-6vs8:
Mycobacterium tuberculosis dihydrofolate reductase in complex with ethyl 2-methyl thiazole-4-carboxylate(fragment 3)
Method: X-RAY DIFFRACTION / Resolution: 1.829 Å

PDB-6vs9:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(piperidin-1-ylmethyl)benzoic acid(fragment 11)
Method: X-RAY DIFFRACTION / Resolution: 1.842 Å

PDB-6vsd:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-((thiophen-2-ylthio)methyl)benzoic acid (fragment 13)
Method: X-RAY DIFFRACTION / Resolution: 1.693 Å

PDB-6vse:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(phenoxymethyl)benzoic acid(fragment 14)
Method: X-RAY DIFFRACTION / Resolution: 1.758 Å

PDB-6vsf:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)-4-oxobutanoic acid(fragment 16)
Method: X-RAY DIFFRACTION / Resolution: 2.012 Å

PDB-6vsg:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(trifluoromethyl)benzene-1,2-diamine(fragment 17)
Method: X-RAY DIFFRACTION / Resolution: 2.304 Å

PDB-6vv6:
Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB113
Method: X-RAY DIFFRACTION / Resolution: 2.235 Å

PDB-6vv7:
Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB136
Method: X-RAY DIFFRACTION / Resolution: 1.999 Å

PDB-6vv8:
Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB285
Method: X-RAY DIFFRACTION / Resolution: 2.683 Å

PDB-6vv9:
Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB300
Method: X-RAY DIFFRACTION / Resolution: 2.18 Å

PDB-6vvb:
Mycobacterium tuberculosis dihydrofolate reductase in complex with 6-methyl-5-(4-phenylthiazol-2-yl)-2- (trifluoromethyl)nicotinic acid (fragment 10)
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

Chemicals

ChemComp-CO:
Unknown entry

ChemComp-9FH:
5-methyl-1-phenyl-pyrazole-4-carboxylic acid

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

ChemComp-RKV:
3-(furan-2-yl)-1-methyl-1H-pyrazole-5-carboxylic acid

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-RJY:
ethyl 2-methyl-1,3-thiazole-4-carboxylate

ChemComp-SO4:
SULFATE ION

ChemComp-RK4:
3-[(piperidin-1-yl)methyl]benzoic acid

ChemComp-GOL:
GLYCEROL

ChemComp-JBB:
3-(thiophen-2-ylsulfanylmethyl)benzoic acid

ChemComp-4RG:
3-(phenoxymethyl)benzoic acid

ChemComp-RKY:
4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid

ChemComp-X0V:
4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE

ChemComp-RPJ:
1-(4-fluorophenyl)-5-[3-(1H-indol-3-yl)propoxy]-1H-pyrazole-4-carboxylic acid

ChemComp-RPM:
5-[3-(5-methyl-1H-indol-3-yl)propoxy]-1-phenyl-1H-pyrazole-4-carboxylic acid

ChemComp-RPV:
5-{[3-(1H-indol-3-yl)propanoyl]amino}-1-phenyl-1H-pyrazole-4-carboxylic acid

ChemComp-RQ1:
5-[4-(1H-indol-3-yl)butoxy]-1-phenyl-1H-pyrazole-4-carboxylic acid

ChemComp-RQ4:
6-methyl-5-(4-phenyl-1,3-thiazol-2-yl)-2-(trifluoromethyl)pyridine-3-carboxylic acid

ChemComp-P33:
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / precipitant*YM

Source
  • mycobacterium tuberculosis (bacteria)
  • mycobacterium tuberculosis (strain atcc 25177 / h37ra) (bacteria)
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
KeywordsBIOSYNTHETIC PROTEIN / folate pathway / OXIDOREDUCTASE

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