Brand  (β version)

PDB ID: 5TUQ

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Ligands
Code Name Style Show Link
J63 1-[(benzyloxy)methyl]-6-(cyclohexylmethyl)-3-hydroxy-5-(propan-2-yl)pyrimidine-2,4(1h,3h)-dione PoSSuM
MG Magnesium ion PoSSuM
Non-standard Residues
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Structure summary

Code : 5TUQ   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/TRANSFERASE INHIBITOR
Title : Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione Inhibitor in Complex with HIV Reverse Transcriptase
Release Data : 2017-06-28
Compound :
mol_id molecule chains synonym
1 HIV-1 REVERSE TRANSCRIPTASE A Pr160Gag-Pol
ec: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2
fragment: p66 domain residues 600-1154
mutation: C280S
mol_id molecule chains synonym
2 HIV-1 REVERSE TRANSCRIPTASE B Pr160Gag-Pol
ec: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2
fragment: p51 domain residues 600-1027
mutation: C280S
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1 group M subtype B (isolate BH10)  (taxid:11678) HIV-1 Escherichia coli  (taxid:469008)
strain: isolate BH10
gene: gag-pol
expression_system_strain: BL21 (DE3) RIL
expression_system_vector_type: plasmid
expression_system_plasmid: pET35a
mol_id organism_scientific organism_common expression_system
2 Human immunodeficiency virus type 1 group M subtype B (isolate BH10)  (taxid:11678) HIV-1 Escherichia coli  (taxid:469008)
strain: isolate BH10
gene: gag-pol
expression_system_strain: BL21 (DE3) RIL
expression_system_vector_type: plasmid
expression_system_plasmid: pET35a
Authors : Kirby, K.A., Sarafianos, S.G.
Keywords : HIV-1, REVERSE TRANSCRIPTASE, INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 2.7050 Å )
Citation :

6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase.

Tang, J.,Kirby, K.A.,Huber, A.D.  et al.
(2017)  Eur J Med Chem  128 : 168 - 179

PubMed: 28182989
DOI: 10.1016/j.ejmech.2017.01.041

Reaction

Chain : B
UniProt : P03366 (POL_HV1B1)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
-
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
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[Reverse transcriptase/ribonuclease H]
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. 		3.1.26.13 PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.49 PROSITE- ProRule:PRU00405, PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.7 PROSITE- ProRule:PRU00405, PubMed:2476069
-