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 
Experimental Data Snapshot
Starting Model: experimental
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(2018) European J Org Chem 
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
5'(3')-deoxyribonucleotidase, cytosolic type | 205 | Homo sapiens | Mutation(s): 0  Gene Names: NT5C, DNT1, UMPH2 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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8TCD5 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
O84 Query on O84 | D [auth A], F [auth B] | [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]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 C19 H22 N2 O11 P2 TZXVMSWLUKAZDT-PDBOZARJSA-N | |||
MG Query on MG | C [auth A], E [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
CME Query on CME | A, B | L-PEPTIDE LINKING | C5 H11 N O3 S2 | CYS |
Length ( Å ) | Angle ( ˚ ) |
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a = 38.877 | α = 67.86 |
b = 47.231 | β = 88.69 |
c = 61.795 | γ = 77.37 |
Software Name | Purpose |
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XDS | data reduction |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Funding Organization | Location | Grant Number |
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Grant Agency of the Czech Republic | Czech Republic | 203-09-0820 |
Grant Agency of the Czech Republic | Czech Republic | 15-05677S |
Czech Science Foundation | Czech Republic | 17-12703S |