6DWD

SAMHD1 Bound to Clofarabine-TP in the Catalytic Pocket and Allosteric Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 

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 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GLY
Query on GLY

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A, B, C, D
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SIN
Query on SIN

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B, D
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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B, C, D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
HDV
Query on HDV

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A, B, C, D
9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-methyl-9H-purin-6-amine
Clofarabine-TRIPHOSPHATE
C11 H17 F N5 O12 P3
BGNIGZFVXIGOQD-WCGPTHBMSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TCE
Query on TCE

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Download CCD File 
A
3,3',3''-phosphanetriyltripropanoic acid
3-[bis(2-carboxyethyl)phosphanyl]propanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.477α = 90.00
b = 142.233β = 114.10
c = 98.790γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

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