[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleChemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Journal, issue, pagesEur. J. Med. Chem., Vol. 247, Page 115035-115035, Year 2023
Publish dateDec 6, 2019 (structure data deposition date)
AuthorsSlavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. ...Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
External linksEur. J. Med. Chem. / PubMed:36603507
MethodsX-ray diffraction
Resolution2.23 - 2.89 Å
Structure data

PDB-6v6x:
The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000988632
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-6v9e:
The crystal structure of the 2009 H1N1 PA endonuclease wild type in complex with SJ000988632
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-6vbr:
The crystal structure of the 2009 H1N1/California PA endonuclease wild type in complex with SJ000986248
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-6vg9:
The crystal structure of the 2009 H1N1/California PA endonuclease I38T mutant in complex with SJ000986248
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-6viv:
The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986192
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-6vjh:
The crystal structure of the 2009 H1N1/California PA endonuclease wild type in complex with SJ000986192
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-6vl3:
The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986436
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

PDB-6wij:
The crystal structure of the 2009/H1N1/California PA endonuclease mutant I38T in complex with SJ000986448
Method: X-RAY DIFFRACTION / Resolution: 2.44 Å

PDB-6wj4:
The crystal structure of the 2009/H1N1/California PA endonuclease wild type in complex with SJ000986448
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-7k87:
The crystal structure of the 2009 H1N1 PA endonuclease in complex with SJ000986436
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-7lm4:
The crystal structure of the I38T mutant PA Endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503
Method: X-RAY DIFFRACTION / Resolution: 2.35 Å

PDB-7lw6:
The crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with Raltegravir
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-7m0n:
The crystal structure of wild type PA endonuclease (A/Vietnam/1203/2004) in complex with Raltegravir
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-7mpf:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000986436
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-7mty:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988569
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-7n47:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988514
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-7n55:
The crystal structure of the mutant I38T PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988514
Method: X-RAY DIFFRACTION / Resolution: 2.33 Å

PDB-7n68:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988288
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

PDB-7n8f:
The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988288
Method: X-RAY DIFFRACTION / Resolution: 2.35 Å

PDB-7rkp:
The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with cyclic compound SJ001034733
Method: X-RAY DIFFRACTION / Resolution: 2.36 Å

PDB-7umr:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001034732-1 (trans-form)
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

PDB-7uuh:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001034732-2 (cis-form)
Method: X-RAY DIFFRACTION / Resolution: 2.89 Å

PDB-8dip:
The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023030
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-8dpj:
The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023030
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-8dtw:
The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023036
Method: X-RAY DIFFRACTION / Resolution: 2.33 Å

PDB-8e4s:
The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023034
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-QQP:
N-[2-(6-amino-9H-purin-9-yl)ethyl]-5-hydroxy-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide

ChemComp-QQ4:
Hexa Vinylpyrrolidone K15

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-Y24:
1,1',1'',1''',1''''-[(3R,5S,7S,9R)-decane-1,3,5,7,9-pentayl]penta(pyrrolidin-2-one)

ChemComp-QVV:
benzyl [2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate

ChemComp-QZM:
2-[2-[(cyclohexylmethyl-$l^{3}-oxidanyl)carbonylamino]propan-2-yl]-~{N}-[2-(5-methoxy-4-oxidanyl-cyclohexa-1,3,5-trien-1-yl)ethyl]-5-oxidanyl-6-oxidanylidene-pyrimidine-4-carboxamide

ChemComp-R1D:
5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide

ChemComp-U3A:
5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide

ChemComp-W5V:
2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide

ChemComp-Y5V:
5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide

ChemComp-RLT:
N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di / medication, antiretroviral*YM

ChemComp-GOL:
GLYCEROL

ChemComp-09Y:
5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide

ChemComp-0VL:
benzyl {2-[(5S)-5-hydroxy-4-oxo-6-{[2-(pyridin-4-yl)ethyl]carbamoyl}-4,5-dihydropyrimidin-2-yl]propan-2-yl}carbamate

ChemComp-R3J:
benzyl [2-(5-hydroxy-4-{[2-(2-methoxypyridin-4-yl)ethyl]carbamoyl}-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate

ChemComp-5Y1:
(5R)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2,6(28),11(27),12,14,22,24-octaene-4,7-dione

ChemComp-NVR:
(1P,18Z)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2(28),5,11(27),12,14,18,22,24-nonaene-4,7-dione

ChemComp-SE9:
(2P)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide

ChemComp-TLR:
5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-{[2-(trifluoromethyl)phenyl]methyl}-1,6-dihydropyrimidine-4-carboxamide

ChemComp-MG:
Unknown entry

ChemComp-U9U:
5-hydroxy-6-oxo-N-[2-(pyridin-4-yl)ethyl]-2-{[2-(trifluoromethyl)phenyl]methyl}-3,6-dihydropyrimidine-4-carboxamide

Source
  • influenza a virus (a/luxembourg/43/2009(h1n1))
  • influenza a virus
  • influenza a virus (strain swl a/california/04/2009 h1n1)
  • influenza a virus (a/ruddy turnstone/new jersey/sg-00524/2008(h4n6))
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / HYDROLASE / VIRAL PROTEIN/Inhibitor / VIRAL PROTEIN-Inhibitor complex / HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Hydrolase/Inhibitor / Hydrolase-Inhibitor complex

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more