4RT2 image
Deposition Date 2014-11-12
Release Date 2015-07-01
Last Version Date 2023-09-20
Entry Detail
PDB ID:
4RT2
Keywords:
Title:
Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.92 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:A
Chain Length:335
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*CP*GP*G)-3')
Chain IDs:D
Chain Length:5
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
Chain IDs:C (auth: P)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Chain IDs:B (auth: T)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
DOC C DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
Primary Citation
Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP.
Org.Lett. 17 2586 2589 (2015)
PMID: 25970636 DOI: 10.1021/acs.orglett.5b00799

Abstact

Novel α,β-CH2 and β,γ-NH (1a) or α,β-NH and β,γ-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase β, attributed to an NH-group interaction with R183 in the active site.

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Primary Citation of related structures
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