Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF320 inhibitor

Experimental Data Snapshot

  • Resolution: 2.64 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.

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.

(2024) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.3c00613
  • Primary Citation of Related Structures:  
    8GKS, 8GKT, 8GKU, 8GKW, 8GKY, 8GKZ, 8T4O, 8T4P, 8TLC

  • PubMed Abstract: 

    We previously discovered first-in-class multitargeted 5-substituted pyrrolo[3,2- d ]pyrimidine antifolates that inhibit serine hydroxymethyltransferase 2 (SHMT2), resulting in potent in vitro and in vivo antitumor efficacies. In this report, we present crystallographic structures for SHMT2 in complex with an expanded series of pyrrolo[3,2- d ]pyrimidine compounds with variations in bridge length (3-5 carbons) and the side chain aromatic ring (phenyl, thiophene, fluorine-substituted phenyl, and thiophene). We evaluated structural features of the inhibitor-SHMT2 complexes and correlations to inhibitor potencies (i.e., K i s), highlighting conserved polar contacts and identifying 5-carbon bridge lengths as key determinants of inhibitor potency. Based on the analysis of SHMT2 structural data, we investigated the impact of mutation of Tyr105 in SHMT2 kinetic analysis and studies with HCT116 cells with inducible expression of wild-type and Y105F SHMT2. Increased enzyme inhibition potency by the pyrrolo[3,2- d ]pyrimidine inhibitors with Phe105 SHMT2 accompanied an increased growth inhibition of Phe105-expressing HCT116 cells compared to wild-type SHMT2. Pyrrolo[3,2- d ]pyrimidine inhibitors with polyglutamate modifications were evaluated for potencies against SHMT2. We determined the crystal structures of SHMT2 in complex with our lead antifolate AGF347 lacking L-glutamate, or as a diglutamate and triglutamate, for comparison with parent AGF347. These data provide the first insights into the influence of antifolate polyglutamylation on SHMT2:inhibitor interactions. Collectively, our results provide new insights into the critical structural determinants of SHMT2 binding by pyrrolo[3,2- d ]pyrimidine inhibitors as novel antitumor agents, as well as the first structural characterization of human SHMT2 in complex with polyglutamates of an SHMT2-targeted antifolate.

  • Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, mitochondrial
A, B
493Homo sapiensMutation(s): 0 
Gene Names: SHMT2
UniProt & NIH Common Fund Data Resources
Find proteins for P34897 (Homo sapiens)
Explore P34897 
Go to UniProtKB:  P34897
PHAROS:  P34897
GTEx:  ENSG00000182199 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34897
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y7L (Subject of Investigation/LOI)
Query on Y7L

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
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
C21 H25 N5 O6 S
Query on PLG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C10 H15 N2 O7 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.64 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.196α = 90
b = 158.196β = 90
c = 207.279γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA250469

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release