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Structure paper

TitleFragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.
Journal, issue, pagesNucleic Acids Res., Vol. 48, Page 8099-8112, Year 2020
Publish dateFeb 5, 2019 (structure data deposition date)
AuthorsThomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. ...Thomas, S.E. / Whitehouse, A.J. / Brown, K. / Burbaud, S. / Belardinelli, J.M. / Sangen, J. / Lahiri, R. / Libardo, M.D.J. / Gupta, P. / Malhotra, S. / Boshoff, H.I.M. / Jackson, M. / Abell, C. / Coyne, A.G. / Blundell, T.L. / Floto, R.A. / Mendes, V.
External linksNucleic Acids Res. / PubMed:32602532
MethodsX-ray diffraction
Resolution1.48 - 3.06 Å
Structure data

PDB-6nvr:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in Apo form
Method: X-RAY DIFFRACTION / Resolution: 1.562 Å

PDB-6nw6:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with S-Adenosyl methionine
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-6nw7:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with S-Adenosyl-L-homocysteine
Method: X-RAY DIFFRACTION / Resolution: 1.481 Å

PDB-6qo2:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 1 (1H-Indole-5-carboxamide)
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-6qo3:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 2 (5-Amino-3-(2-thienyl) pyrazole)
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-6qo4:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 3 (2-(5-Isoxazolyl) phenol)
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-6qo6:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 4 (5-Methoxybenzimidazole)
Method: X-RAY DIFFRACTION / Resolution: 1.745 Å

PDB-6qoa:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 5 (Isoxazole-5-carboxamide)
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-6qoc:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 6 (2-(1,3-oxazol-5-yl) aniline)
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-6qod:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 7 (2-Amino-6-fluorobenzothiazole)
Method: X-RAY DIFFRACTION / Resolution: 1.852 Å

PDB-6qoe:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 8 (3-[(2-thienylthio)methyl]benzoic acid)
Method: X-RAY DIFFRACTION / Resolution: 3.06 Å

PDB-6qof:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 9 (Adenine)
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-6qog:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 10 (2-Amino-5-bromobenzothiazole)
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6qoh:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 11 (2-Amino-6-chloropurine)
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-6qoi:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 12 (2-Aminobenzothiazole)
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-6qoj:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 13 (4-Hydroxyquinazoline)
Method: X-RAY DIFFRACTION / Resolution: 2.023 Å

PDB-6qok:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 14 (Methyl 2-aminopyridine-4-carboxylate)
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-6qol:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 15 (6-quinoxalinamine)
Method: X-RAY DIFFRACTION / Resolution: 1.903 Å

PDB-6qom:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 16 (2-Amino-3-nitropyridine)
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-6qon:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 17 (2H-1,3-Benzoxazine-2,4(3H)-dione)
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-6qoo:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 18 (Isoxazole-5-carbothioamide)
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-6qop:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 19 (5-fluoroquinazolin-4-ol)
Method: X-RAY DIFFRACTION / Resolution: 1.912 Å

PDB-6qoq:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 20 (6-Aminobenzothiazole)
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-6qor:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 21 (2-Amino-3-nitrophenol)
Method: X-RAY DIFFRACTION / Resolution: 1.671 Å

PDB-6qos:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 22 (Ethyl 1H-pyrazole-4-carboxylate)
Method: X-RAY DIFFRACTION / Resolution: 2.052 Å

PDB-6qot:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 23 (3-Amino-5-(4-methoxyphenyl)pyrazole)
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-6qou:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 24 (Indole-6-boronic acid)
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-6qov:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 25 (6-Phenyl-3-pyridinyl)methylamine)
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6qow:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 26 (6-methoxybenzothiazole-2-carboxylic acid)
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-6qox:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 27 (Methyl 2-(hydroxymethyl)-6H-thieno[2,3-b]pyrrole-5-carboxylate)
Method: X-RAY DIFFRACTION / Resolution: 1.74 Å

PDB-6qqs:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-6qqx:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.69 Å

PDB-6qqy:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-6qr5:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-6qr6:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-6qr8:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

ChemComp-JAW:
1~{H}-indole-5-carboxamide

ChemComp-J9N:
3-thiophen-2-yl-1H-pyrazol-5-amine

ChemComp-97T:
2-(1,2-oxazol-5-yl)phenol

ChemComp-5OB:
5-METHOXYBENZIMIDAZOLE

ChemComp-JBN:
1,2-oxazole-5-carboxamide

ChemComp-J9Q:
2-(1,3-oxazol-5-yl)aniline

ChemComp-FBB:
6-fluoro-1,3-benzothiazol-2-amine

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

ChemComp-ADE:
ADENINE / Adenine

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-JA8:
5-bromanyl-1,3-benzothiazol-2-amine

ChemComp-6GU:
6-chloroguanine

ChemComp-ABV:
1,3-benzothiazol-2-amine

ChemComp-JBH:
3,4-dihydroquinazolin-4-ol

ChemComp-J9T:
methyl 2-azanylpyridine-4-carboxylate

ChemComp-JB5:
quinoxalin-6-amine

ChemComp-JBE:
3-nitropyridin-2-amine

ChemComp-J9W:
1,3-benzoxazine-2,4-dione

ChemComp-JAB:
1,2-oxazole-5-carbothioamide

ChemComp-JBQ:
5-fluoranyl-3,4-dihydroquinazolin-4-ol

ChemComp-JAE:
1,3-benzothiazol-6-amine

ChemComp-JBK:
2-azanyl-3-nitro-phenol

ChemComp-GOJ:
ethyl 1~{H}-pyrazole-4-carboxylate

ChemComp-6SD:
3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine

ChemComp-JB8:
1~{H}-indol-6-ylboronic acid

ChemComp-JAH:
(6-phenylpyridin-3-yl)methanamine

ChemComp-JBZ:
6-methoxy-1,3-benzothiazole-2-carboxylic acid

ChemComp-JA5:
methyl 2-(hydroxymethyl)-6~{H}-thieno[2,3-b]pyrrole-5-carboxylate

ChemComp-JCZ:
3-(1~{H}-indol-6-yl)-1~{H}-pyrazol-5-amine

ChemComp-JCE:
5-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazol-3-amine

ChemComp-JD2:
5-azanyl-3-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile

ChemComp-JFH:
3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine

ChemComp-JCK:
5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile

ChemComp-JDH:
5-azanyl-3-[1-[[4-[(4-methylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile

Source
  • mycobacteroides abscessus (bacteria)
  • mycobacterium abscessus (bacteria)
KeywordsTRANSFERASE / TrmD / tRNA methyltransferase / SPOUT methyltransferase

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