5V7I Transferase Transferase Inhibitor date Mar 20, 2017
title Crystal Structure Of Homo Sapiens Serine Hydroxymethyltransf (Mitochondrial) (Shmt2), In Complex With Glycine, Plp And F Competitive Pyrazolopyran Inhibitor: 6-Amino-4-Isopropyl-3- (3-(Pyrrolidin-1-Yl)-5-(Trifluoromethyl)Phenyl)-1,4-Dihydro 3-C]Pyrazole-5-Carbonitrile
authors G.S.Ducker, J.M.Ghergurovich, N.Mainolfi, V.Suri, S.Jeong, A.Frie M.Manfredi, H.Kim, J.D.Rabinowitz
compound source
Molecule: Serine Hydroxymethyltransferase, Mitochondrial
Chain: A, B
Synonym: Shmt,Glycine Hydroxymethyltransferase,Serine Methy
Ec: 2.1.2.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Shmt2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 65 2 2
R_factor 0.202 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.140 160.140 210.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.47 Å
ligand 8Z1, GLY, GOL, LLP, PEG enzyme Transferase E.C.2.1.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • translation repressor activi...


  • Primary referenceHuman SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma., Ducker GS, Ghergurovich JM, Mainolfi N, Suri V, Jeong SK, Hsin-Jung Li S, Friedman A, Manfredi MG, Gitai Z, Kim H, Rabinowitz JD, Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11404-11409. doi:, 10.1073/pnas.1706617114. Epub 2017 Oct 9. PMID:29073064
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (5v7i.pdb1.gz) 157 Kb
  • LPC: Ligand-Protein Contacts for 5V7I
  • CSU: Contacts of Structural Units for 5V7I
  • Structure Factors (1702 Kb)
  • Retrieve 5V7I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V7I from S2C, [Save to disk]
  • View 5V7I in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5V7I
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v7i_B] [5v7i_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V7I
  • Community annotation for 5V7I at PDBWiki (http://pdbwiki.org)

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