6DW5

SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 

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
A, B, C, D
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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTF
Query on GTF

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Download CCD File 
A, B, C, D
2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)
Gemcitabine-TRIPHOSPHATE
C9 H14 F2 N3 O13 P3
YMOXEIOKAJSRQX-QPPQHZFASA-N
 Ligand Interaction
DTP
Query on DTP

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

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Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, B, 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
NI
Query on NI

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Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.686α = 90.00
b = 142.901β = 113.92
c = 98.907γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
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