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Structure paper

TitleFragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases.
Journal, issue, pagesBioorg. Med. Chem., Vol. 44, Page 116283-116283, Year 2021
Publish dateMar 5, 2021 (structure data deposition date)
AuthorsAkaki, T. / Bessho, Y. / Ito, T. / Fujioka, S. / Ubukata, M. / Mori, G. / Yamanaka, K. / Orita, T. / Doi, S. / Iwanaga, T. ...Akaki, T. / Bessho, Y. / Ito, T. / Fujioka, S. / Ubukata, M. / Mori, G. / Yamanaka, K. / Orita, T. / Doi, S. / Iwanaga, T. / Ikegashira, K. / Hantani, Y. / Nakanishi, I. / Adachi, T.
External linksBioorg. Med. Chem. / PubMed:34274549
MethodsX-ray diffraction
Resolution1.9 - 2.34 Å
Structure data

PDB-7ea0:
Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 1
Method: X-RAY DIFFRACTION / Resolution: 2.34 Å

PDB-7eas:
Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7eat:
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 1
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7ebb:
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 2
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7ebg:
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7ebh:
Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

Chemicals

ChemComp-CL:
Unknown entry

ChemComp-ACT:
ACETATE ION

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-W6P:
1,3-dihydro-2H-indol-2-one

ChemComp-HOH:
WATER

ChemComp-42A:
1H-pyrrolo[2,3-b]pyridine-3-carbonitrile

ChemComp-SO4:
SULFATE ION

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-J0L:
3,3-dimethyl-7-(methylamino)-1H-indol-2-one

ChemComp-J0F:
5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine

Source
  • homo sapiens (human)
KeywordsTRANSFERASE/INHIBITOR / PDHK / KINASE INHIBITORS / FRAGMENT SCREENING / PDK1 / PDK2 / PDK3 / PDK4 / TRANSFERASE-INHIBITOR complex / TRANSFERASE

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