6DWK | pdb_00006dwk

SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket

• PDB DOI: https://doi.org/10.2210/pdb6DWK/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-06-26 Released: 2018-10-10 
• Deposition Author(s): Knecht, K.M., Buzovetsky, O., Schneider, C., Thomas, D., Srikanth, V., Kaderali, L., Tofoleanu, F., Reiss, K., Ferreiros, N., Geisslinger, G., Batista, V.S., Ji, X., Cinatl, J., Keppler, O.T., Xiong, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1.

Knecht, K.M., Buzovetsky, O., Schneider, C., Thomas, D., Srikanth, V., Kaderali, L., Tofoleanu, F., Reiss, K., Ferreiros, N., Geisslinger, G., Batista, V.S., Ji, X., Cinatl Jr., J., Keppler, O.T., Xiong, Y.

(2018) Proc Natl Acad Sci U S A 115: E10022-E10031

• PubMed: 30305425 
• DOI: https://doi.org/10.1073/pnas.1805593115
• Primary Citation Related Structures: 
  6DW3, 6DW4, 6DW5, 6DW7, 6DWD, 6DWJ, 6DWK


• PubMed Abstract: 
  

  SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in noncycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analog drugs important for treating a variety of cancers, including acute myeloid leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We found that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogs tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regard to nucleotide analogs, which can be used to improve current cancer and antiviral therapies.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.
Institute of Medical Virology, University Hospital Frankfurt, 60596 Frankfurt, Germany.
Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, Goethe University of Frankfurt, 60590 Frankfurt, Germany.
Zentrum für Arzneimittelforschung, -entwicklung, und -sicherheit, Goethe University of Frankfurt, 60590 Frankfurt, Germany.
Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany.
Department of Chemistry, Yale University, New Haven, CT 06520.
National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Project Group Translational Medicine and Pharmacology, Frauenhofer Institute for Molecular Biology and Applied Ecology, 60590 Frankfurt, Germany.
The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 Jiangsu, China.
Max von Pettenkofer-Institute, Department of Virology, Ludwig Maximilians University, 80336 Munich, Germany.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 261.85 kDa 
• Atom Count: 16,439 
• Modeled Residue Count: 1,914 
• Deposited Residue Count: 2,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1	A, B, C, D	550	Homo sapiens	Mutation(s): 2  Gene Names: SAMHD1, MOP5 EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens) Explore Q9Y3Z3  Go to UniProtKB:  Q9Y3Z3
PHAROS:  Q9Y3Z3 GTEx:  ENSG00000101347

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFD	E [auth A], KA [auth C], T [auth B], XA [auth D]	2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine C10 H15 F N5 O13 P3 PIOKUWLZUXUBCO-FJFJXFQQSA-N
GTP	F [auth A], J [auth A], LA [auth C], U [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
DTP	G [auth A], IA [auth C], V [auth B], WA [auth D]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
TRS	FA [auth B], GA [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	KB [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY	DA [auth B], EA [auth B], GB [auth D], HB [auth D], IB [auth D], JB [auth D], QA [auth C], RA [auth C], S [auth A], SA [auth C], TA [auth C], UA [auth C]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
MG	CA [auth B], EB [auth D], FB [auth D], H [auth A], I [auth A], JA [auth C], PA [auth C], R [auth A], VA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CB [auth D], DB [auth D], HA [auth C], K [auth A], L [auth A], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], Q [auth A], W [auth B], X [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.691	α = 90
b = 146.671	β = 114.53
c = 99.131	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Knecht, K.M., Buzovetsky, O., Schneider, C., Thomas, D., Srikanth, V., Kaderali, L., Tofoleanu, F., Reiss, K., Ferreiros, N., Geisslinger, G., Batista, V.S., Ji, X., Cinatl, J., Keppler, O.T., Xiong, Y.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2018-11-07
  Changes: Data collection, Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary