6G2L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases

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

(2018) European J Org Chem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'(3')-deoxyribonucleotidase, mitochondrial202Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EJ8
Query on EJ8

Download Ideal Coordinates CCD File 
D [auth A][(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid
C18 H22 N2 O11 P2 S
KFRRWRABRKBEOD-ATNYBXOESA-N
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
C [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-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: 0.150 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.122 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.797α = 90
b = 73.797β = 90
c = 106.632γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

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 Republic203-09-0820
Grant Agency of the Czech RepublicCzech Republic15-05677S
Czech Science FoundationCzech Republic17-12703S

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description