4YIH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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, cytosolic type
A, B
195Homo sapiensMutation(s): 0 
Gene Names: NT5CDNT1UMPH2
EC: 3.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCD5 (Homo sapiens)
Explore Q8TCD5 
Go to UniProtKB:  Q8TCD5
PHAROS:  Q8TCD5
GTEx:  ENSG00000125458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCD5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2O2
Query on 2O2

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
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
PO4
Query on PO4

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

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.818α = 111.18
b = 46.451β = 88.16
c = 61.738γ = 104.7
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic15-05677S

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 2.0: 2017-09-06
    Changes: Advisory, 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, Derived calculations, Refinement description