[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

TitleAn Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-kappa B-Utilizing a Reversible Covalent Tethering Approach.
Journal, issue, pagesJ. Med. Chem., Vol. 64, Page 8423-8436, Year 2021
Publish dateJan 12, 2021 (structure data deposition date)
AuthorsWolter, M. / Valenti, D. / Cossar, P.J. / Hristeva, S. / Levy, L.M. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C.
External linksJ. Med. Chem. / PubMed:34076416
MethodsX-ray diffraction
Resolution1.2 - 2 Å
Structure data

PDB-7bi3:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-179
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7biq:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-180
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7biw:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-187
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7biy:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-175
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7bjb:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-044
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7bjf:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-069
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7bjl:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-142
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7bjw:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-154
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7bkh:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-153
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nj9:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-133
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7njb:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-132
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nk3:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-128
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nk5:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-124
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nla:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-119
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nle:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-118
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nm1:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-126
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nm3:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-135
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nm9:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-110
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7nmh:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-070
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nr7:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-111
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nv4:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-188
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nvi:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-186
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nws:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-185
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nxs:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-184
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nxt:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-183
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nxw:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-182
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7nxy:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-181
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7ny4:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-130
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nye:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-134
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nyf:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-131
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nyg:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-127
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nz6:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-125
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nzg:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-122
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nzk:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-121
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7nzv:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-120
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o34:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-043
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7o3a:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-046
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7o3f:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-117
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o3p:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-116
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o3q:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-041
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o3r:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-042
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o3s:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-045
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7o57:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-157
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o59:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-192
Method: X-RAY DIFFRACTION / Resolution: 1.2 Å

PDB-7o5a:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-158
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5c:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-159
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5d:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-160
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5f:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-161
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5g:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-164
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5o:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-165
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5p:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-166
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5s:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-167
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5u:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-168
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o5x:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-173
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o6f:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-178
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7o6g:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-176
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o6i:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-085
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7o6j:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-083
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o6k:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-080
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o6m:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-097
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7o6o:
14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-096
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-TQW:
4-[(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)sulfonyl]benzaldehyde

ChemComp-GOL:
GLYCEROL

ChemComp-CA:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-HOH:
WATER

ChemComp-TVB:
4-[[(2~{R})-2-methyl-3,4-dihydro-2~{H}-quinolin-1-yl]sulfonyl]benzaldehyde

ChemComp-TW8:
4-(3,4-dihydro-2~{H}-quinoxalin-1-ylsulfonyl)benzaldehyde

ChemComp-TWE:
1-(4-methanoylphenyl)carbonylpiperidine-4-carbonitrile

ChemComp-TZK:
4-(4-methylphenyl)sulfonylmorpholine

ChemComp-MG:
Unknown entry

ChemComp-TZH:
(5-methyl-2-nitro-phenyl) cyclobutanecarboxylate

ChemComp-TWQ:
3-[(3~{S})-3-methoxypiperidin-1-yl]-4-nitro-benzaldehyde

ChemComp-TZW:
4-nitro-3-(4-oxidanylpiperidin-1-yl)benzaldehyde

ChemComp-U1B:
4-nitro-3-[(3S)-3-oxidanylpiperidin-1-yl]benzaldehyde

ChemComp-UGE:
4-(3,4-dihydro-2~{H}-quinolin-1-ylsulfonyl)benzaldehyde

ChemComp-UG8:
4-piperidin-1-ylsulfonylbenzaldehyde

ChemComp-UGQ:
2-(4-methylphenyl)sulfonyl-3,4-dihydro-1~{H}-isoquinoline

ChemComp-UGN:
1-(4-methylphenyl)sulfonyl-4-(2-methylpropyl)piperazine

ChemComp-UHT:
~{N}-cyclohexyl-4-methanoyl-~{N}-methyl-benzenesulfonamide

ChemComp-UHW:
4-(4-methylpiperazin-1-yl)sulfonylbenzaldehyde

ChemComp-UHN:
4-(4-pyrrolidin-1-ylpiperidin-1-yl)sulfonylbenzaldehyde

ChemComp-UHQ:
4-[4-(dimethylamino)piperidin-1-yl]sulfonylbenzaldehyde

ChemComp-S9E:
6-(2-bromanylimidazol-1-yl)pyridine-3-carbaldehyde

ChemComp-UHZ:
(5-methanoyl-2-nitro-phenyl) methanesulfonate

ChemComp-UON:
4-(2-chloranyl-5-methoxy-benzimidazol-1-yl)benzaldehyde

ChemComp-UOT:
4-(2-chloranyl-6-methoxy-benzimidazol-1-yl)benzaldehyde

ChemComp-UST:
4-(2,3-dihydroindol-1-ylsulfonyl)benzaldehyde

ChemComp-USW:
4-[(7-chloranyl-2,3-dihydro-1,4-benzoxazin-4-yl)sulfonyl]benzaldehyde

ChemComp-UT8:
4-[(7-methoxy-2,3-dihydro-1,4-benzoxazin-4-yl)sulfonyl]benzaldehyde

ChemComp-UVK:
4-[(6-fluoranyl-2,3-dihydro-1,4-benzoxazin-4-yl)sulfonyl]benzaldehyde

ChemComp-UVE:
4-(2,3-dihydro-1,4-benzoxazin-4-ylsulfonyl)benzaldehyde

ChemComp-UVZ:
4-[(6-chloranyl-3,4-dihydro-2~{H}-quinolin-1-yl)sulfonyl]benzaldehyde

ChemComp-UVQ:
4-[(6-fluoranyl-3,4-dihydro-2~{H}-quinolin-1-yl)sulfonyl]benzaldehyde

ChemComp-UVN:
4-(3-oxidanylidenepiperazin-1-yl)sulfonylbenzaldehyde

ChemComp-UVH:
4-(4-propan-2-ylpiperazin-1-yl)sulfonylbenzaldehyde

ChemComp-UVB:
4-[(3~{S})-3-oxidanylpiperidin-1-yl]sulfonylbenzaldehyde

ChemComp-UVT:
4-[(2~{S})-2-methylpyrrolidin-1-yl]sulfonylbenzaldehyde

ChemComp-UWH:
4-[4-(2-methoxyethyl)piperazin-1-yl]sulfonylbenzaldehyde

ChemComp-UWQ:
4-(4-methoxypiperidin-1-yl)sulfonylbenzaldehyde

ChemComp-UWK:
4-[(3~{R})-3-methoxypiperidin-1-yl]sulfonylbenzaldehyde

ChemComp-UXN:
4-methanoyl-N-methyl-N-(oxan-4-yl)benzenesulfonamide

ChemComp-V0Q:
[4-(4-ethylpiperazin-1-yl)sulfonylphenyl]methanol

ChemComp-V0T:
1-[4-(hydroxymethyl)phenyl]sulfonylpiperidin-4-ol

ChemComp-V0W:
1-methyl-4-(4-methylphenyl)sulfonyl-1,4-diazepane

ChemComp-V1K:
2-chloranyl-6-methoxy-1-(4-methylphenyl)sulfonyl-benzimidazole

ChemComp-V1Q:
4-methyl-~{N}-(1-methylpyrazol-3-yl)benzenesulfonamide

ChemComp-V1E:
~{N},~{N},4-trimethylbenzenesulfonamide

ChemComp-V1H:
3-methoxy-1-(4-methylphenyl)sulfonyl-azetidine

ChemComp-V2E:
3-morpholin-4-yl-4-nitro-benzaldehyde

ChemComp-V2N:
4-(6-methoxy-2-methyl-benzimidazol-1-yl)benzaldehyde

ChemComp-V2K:
4-(5-methoxy-2-methyl-benzimidazol-1-yl)benzaldehyde

ChemComp-V2Q:
4-(3-methoxyazetidin-1-yl)carbonylbenzaldehyde

ChemComp-V2T:
4-methanoyl-~{N}-(1-methylpyrazol-3-yl)benzamide

ChemComp-V2W:
4-methanoyl-~{N}-[(4-methoxyphenyl)methyl]benzamide

ChemComp-V32:
4-morpholin-4-ylcarbonylbenzaldehyde

ChemComp-V3B:
4-(4-methanoylphenyl)carbonyl-~{N},~{N}-dimethyl-piperazine-1-carboxamide

ChemComp-V3K:
4-methanoyl-~{N}-[(1-methylpyrazol-4-yl)methyl]benzamide

ChemComp-V3N:
4-methanoyl-~{N}-(oxan-4-ylmethyl)benzamide

ChemComp-V3Q:
4-methanoyl-~{N}-[(3-methoxyphenyl)methyl]benzamide

ChemComp-V3T:
4-methanoyl-~{N}-[(1-methylimidazol-2-yl)methyl]benzamide

ChemComp-V3W:
4-(4-methoxypiperidin-1-yl)carbonylbenzaldehyde

ChemComp-V4K:
4-[4-(2-hydroxyethyl)piperidin-1-yl]carbonylbenzaldehyde

ChemComp-V4H:
4-[(3~{R})-3-oxidanylpiperidin-1-yl]carbonylbenzaldehyde

ChemComp-V4B:
[5-methanoyl-2-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl] 2-methyl-6-(trifluoromethyl)pyridine-3-carboxylate

ChemComp-V48:
(5-methanoyl-2-nitro-phenyl) 2-(3-methoxyphenyl)ethanoate

ChemComp-V4N:
(5-methanoyl-2-nitro-phenyl) 3-chloranylbenzoate

ChemComp-V42:
(5-methanoyl-2-nitro-phenyl) 1-methylpyrazole-4-sulfonate

ChemComp-V3Z:
(5-methanoyl-2-nitro-phenyl) propane-2-sulfonate

Source
  • homo sapiens (human)
KeywordsPEPTIDE BINDING PROTEIN / benzaldehyde / covalent fragment / p65 / 1433 / RelA / imine formation

+
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