6DW3

SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D, C, B, A
550Homo sapiensMutation(s): 2 
Gene Names: SAMHD1 (MOP5)
EC: 3.1.5.-
Find proteins for Q9Y3Z3 (Homo sapiens)
Go to Gene View: SAMHD1
Go to UniProtKB:  Q9Y3Z3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, B, C, D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HF4
Query on HF4

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Download CCD File 
A, B, C, D
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one
Cytarabine-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-CCXZUQQUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.340α = 90.00
b = 147.325β = 114.64
c = 98.537γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-11-07
    Type: Data collection, Database references