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Structure paper

TitleStructural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Journal, issue, pagesBiochemistry, Year 2024
Publish dateMar 20, 2023 (structure data deposition date)
AuthorsKatinas, J.M. / Nayeen, M.J. / Schneider, M. / Shah, K. / Fifer, A.N. / Klapper, L.M. / Sharma, A. / Thalluri, K. / Van Nieuwenhze, M.S. / Hou, Z. ...Katinas, J.M. / Nayeen, M.J. / Schneider, M. / Shah, K. / Fifer, A.N. / Klapper, L.M. / Sharma, A. / Thalluri, K. / Van Nieuwenhze, M.S. / Hou, Z. / Gangjee, A. / Matherly, L.H. / Dann 3rd, C.E.
External linksBiochemistry / PubMed:38324671
MethodsX-ray diffraction
Resolution2.38 - 3.06 Å
Structure data

PDB-8gks:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF291 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.99 Å

PDB-8gkt:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF320 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.64 Å

PDB-8gku:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF355 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 3.06 Å

PDB-8gkw:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF359 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-8gky:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) Y105F in complex with PLP, glycine and AGF359 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.77 Å

PDB-8gkz:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) Y105F in complex with PLP, glycine and AGF362 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-8t4o:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor with no glutamate
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

PDB-8t4p:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and di-glutamate AGF347 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.801 Å

PDB-8tlc:
Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and tri-glutamate AGF347 inhibitor
Method: X-RAY DIFFRACTION / Resolution: 2.72 Å

Chemicals

ChemComp-GLY:
GLYCINE

ChemComp-Y6U:
N-{4-[3-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)propyl]benzoyl}-L-glutamic acid

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

ChemComp-HOH:
WATER

ChemComp-PLG:
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]

ChemComp-Y7L:
N-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid


ChemComp, No image

ChemComp-ZV1:
Unknown entry


ChemComp, No image

ChemComp-ZVR:
Unknown entry

ChemComp-Y72:
N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-3-fluorothiophene-2-carbonyl}-L-glutamic acid


ChemComp, No image

ChemComp-Y5C:
Unknown entry


ChemComp, No image

ChemComp-Y5Z:
Unknown entry


ChemComp, No image

ChemComp-I6I:
Unknown entry

Source
  • homo sapiens (human)
KeywordsTRANSFERASE/INHIBITOR / SHMT2 / tetramer / glycine synthesis / inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex / SHMT2 mutant / Mitochondrial / one-carbon metabolism / polyglutamate / complex / serine and glycine metabolism

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