6DWK

SAMHD1 Bound to Fludarabine-TP in the Catalytic Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1073/pnas.1805593115
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
A, B, C, D
550Homo sapiensMutation(s): 2 
Gene Names: SAMHD1MOP5
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3Z3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HFD
Query on HFD

Download Ideal Coordinates CCD File 
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
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth A],
LA [auth C],
U [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
DTP
Query on DTP

Download Ideal Coordinates CCD File 
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
Query on TRS

Download Ideal Coordinates CCD File 
FA [auth B],
GA [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4
Query on PO4

Download Ideal Coordinates CCD File 
KB [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY
Query on GLY

Download Ideal Coordinates CCD File 
DA [auth B]
EA [auth B]
GB [auth D]
HB [auth D]
IB [auth D]
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
Query on MG

Download Ideal Coordinates CCD File 
CA [auth B]
EB [auth D]
FB [auth D]
H [auth A]
I [auth A]
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
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CB [auth D]
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 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.691α = 90
b = 146.671β = 114.53
c = 99.131γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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