7S2Y

SAMHD1 HD domain bound to CNDAC

PDB DOI: https://doi.org/10.2210/pdb7S2Y/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-09-04 Released: 2021-10-27
Deposition Author(s): Digianantonio, K.M., Xiong, Y.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.232
R-Value Work: 0.186
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Literature

Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells.

Rothenburger, T., Thomas, D., Schreiber, Y., Wratil, P.R., Pflantz, T., Knecht, K., Digianantonio, K., Temple, J., Schneider, C., Baldauf, H.M., McLaughlin, K.M., Rothweiler, F., Bilen, B., Farmand, S., Bojkova, D., Costa, R., Ferreiros, N., Geisslinger, G., Oellerich, T., Xiong, Y., Keppler, O.T., Wass, M.N., Michaelis, M., Cinatl Jr., J.

(2021) J Exp Clin Cancer Res 40: 317-317

PubMed: 34641952 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s13046-021-02093-4
Primary Citation of Related Structures:
7S2Y

PubMed Abstract:
SAMHD1 mediates resistance to anti-cancer nucleoside analogues, including cytarabine, decitabine, and nelarabine that are commonly used for the treatment of leukaemia, through cleavage of their triphosphorylated forms. Hence, SAMHD1 inhibitors are promising candidates for the sensitisation of leukaemia cells to nucleoside analogue-based therapy. Here, we investigated the effects of the cytosine analogue CNDAC, which has been proposed to be a SAMHD1 inhibitor, in the context of SAMHD1.

Organizational Affiliation

Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 259.93 kDa
Atom Count: 16,311
Modelled Residue Count: 1,924
Deposited Residue Count: 2,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y3Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain V [auth D] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D]	I [auth B], O [auth C], T [auth D], V [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain I [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain V [auth D] Interactions & Density Focus chain I [auth B] Focus chain O [auth C] Focus chain T [auth D] Focus chain V [auth D]
85T (Subject of Investigation/LOI) Query on 85T Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain W [auth D]	E [auth A], J [auth B], P [auth C], W [auth D]	4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one C₁₀ H₁₅ N₄ O₁₃ P₃ DZFZBFCEJVKCLY-JWIUVKOKSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain W [auth D]
DTP Query on DTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth D]	F [auth A], K [auth B], N [auth C], U [auth D]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain U [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D]	G [auth A] H [auth A] L [auth B] M [auth B] Q [auth C] G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D]