4YIK

Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor

Pachl, P.Simak, O.Rezacova, P.Fabry, M.Budesinsky, M.Rosenberg, I.Brynda, J.

(2015) Medchemcomm 6: 1635-1638


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'(3')-deoxyribonucleotidase, mitochondrial201Homo sapiensMutation(s): 0 
Gene Names: NT5MDNT2
EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPB1 (Homo sapiens)
Explore Q9NPB1 
Go to UniProtKB:  Q9NPB1
PHAROS:  Q9NPB1
GTEx:  ENSG00000205309 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPB1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2O2
Query on 2O2

Download Ideal Coordinates CCD File 
G [auth A]1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione
C18 H20 N2 O11 P2
AYSYVLQGVXZPIY-OAIWFRFLSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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C [auth A],
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.87α = 90
b = 73.87β = 90
c = 106.19γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic--

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description