6OJU | pdb_00006oju

Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-D-glutamic acid

PDB DOI: https://doi.org/10.2210/pdb6OJU/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-12 Released: 2019-06-19
Deposition Author(s): Czyzyk, D.J., Anderson, K.S., Valhondo, M., Jorgensen, W.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.249 (Depositor), 0.254 (DCC)
R-Value Work:
0.213 (Depositor), 0.221 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase.

Czyzyk, D.J., Valhondo, M., Jorgensen, W.L., Anderson, K.S.

(2019) FEBS Lett 593: 2069-2078

PubMed: 31172516 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.13474
Primary Citation Related Structures:
6OJS, 6OJU, 6OJV

PubMed Abstract:
Thymidylate synthase (TS), found in all organisms, is an essential enzyme responsible for the de novo synthesis of deoxythymidine monophosphate. The TS active sites of the protozoal parasite Cryptosporidium hominis and human are relatively conserved. Evaluation of antifolate compound 1 and its R-enantiomer 2 against both enzymes reveals divergent inhibitor selectivity and enzyme stereospecificity. To establish how C. hominis and human TS (ChTS and hTS) selectively discriminate 1 and 2, respectively, we determined crystal structures of ChTS complexed with 2 and hTS complexed with 1 or 2. Coupled with the previously determined structure of ChTS complexed with 1, we discuss a possible mechanism for enzyme stereospecificity and inhibitor selectivity.

Organizational Affiliation

Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.

Macromolecule Content

Total Structure Weight: 135.64 kDa
Atom Count: 8,992
Modeled Residue Count: 1,140
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase,Thymidylate synthase	A [auth B], B [auth A], C, D	290	Homo sapiens	Mutation(s): 0 Gene Names: TYMS, TS, OK/SW-cl.29 EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens) Explore P04818 Go to UniProtKB: P04818
PHAROS: P04818 GTEx: ENSG00000176890
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04818
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D96 Query on D96 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth B], H [auth A], J [auth C], L [auth D]	N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid C₁₉ H₁₉ N₅ O₆ VDHBMZRBPMTLGE-GFCCVEGCSA-N		Interactions Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth D]
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth B], G [auth A], I [auth C], K [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.249 (Depositor), 0.254 (DCC)
R-Value Work: 0.213 (Depositor), 0.221 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.097	α = 90
b = 124.853	β = 92.12
c = 80.364	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI083146
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5T32AI007404

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2019-08-21
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description