6QVG | pdb_00006qvg

Human SHMT2 in complex with lometrexol

PDB DOI: https://doi.org/10.2210/pdb6QVG/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-01 Released: 2019-09-04
Deposition Author(s): Scaletti, E., Jemth, A.S., Helleday, T., Stenmark, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.236 (Depositor), 0.239 (DCC)
R-Value Work:
0.199 (Depositor), 0.206 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.

Scaletti, E., Jemth, A.S., Helleday, T., Stenmark, P.

(2019) FEBS Lett 593: 1863-1873

PubMed: 31127856 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13455
Primary Citation Related Structures:
6QVG, 6QVL

PubMed Abstract:
Serine hydroxymethyltransferase (SHMT) is the major source of 1-carbon units required for nucleotide synthesis. Humans have cytosolic (SHMT1) and mitochondrial (SHMT2) isoforms, which are upregulated in numerous cancers, making the enzyme an attractive drug target. Here, we show that the antifolates lometrexol and pemetrexed are inhibitors of SHMT2 and solve the first SHMT2-antifolate structures. The antifolates display large differences in their hydrogen bond networks despite their similarity. Lometrexol was found to be the best hSHMT1/2 inhibitor from a panel antifolates. Comparison of apo hSHMT1 with antifolate bound hSHMT2 indicates a highly conserved active site architecture. This structural information offers insights as to how these compounds could be improved to produce more potent and specific inhibitors of this emerging anti-cancer drug target.

Organizational Affiliation

Department of Biochemistry and Biophysics, Stockholm University, Sweden.

Macromolecule Content

Total Structure Weight: 114.07 kDa
Atom Count: 7,607
Modeled Residue Count: 907
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, mitochondrial	A, B	504	Homo sapiens	Mutation(s): 0 Gene Names: SHMT2 EC: 2.1.2.1
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DDF (Subject of Investigation/LOI) Query on DDF Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	5,10-DIDEAZATETRAHYDROFOLIC ACID C₂₁ H₂₅ N₅ O₆ ZUQBAQVRAURMCL-DOMZBBRYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.236 (Depositor), 0.239 (DCC)
R-Value Work: 0.199 (Depositor), 0.206 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.807	α = 90
b = 158.807	β = 90
c = 208.257	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-09-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-04
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Structure summary