7vln - Revision history

OCA at 17:27, 29 November 2023

OCA — Wed, 29 Nov 2023 17:27:53 GMT

←Older revision		Revision as of 17:27, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7vln]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vln]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QC:4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile'>7QC</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.09Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QC:4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile'>7QC</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Wolf-Hirschhorn syndrome. A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH. WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.	+	[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN] Wolf-Hirschhorn syndrome. A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH. WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Histone methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.<ref>PMID:11152655</ref> <ref>PMID:16115125</ref> <ref>PMID:18172012</ref>	+	[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN] Histone methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.<ref>PMID:11152655</ref> <ref>PMID:16115125</ref> <ref>PMID:18172012</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 04:48, 8 September 2022

OCA — Thu, 08 Sep 2022 04:48:22 GMT

←Older revision		Revision as of 04:48, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7vln' size='340' side='right'caption='[[7vln]], [[Resolution\|resolution]] 3.09Å' scene=''>		<StructureSection load='7vln' size='340' side='right'caption='[[7vln]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7vln]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vln]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QC:4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile'>7QC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QC:4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile'>7QC</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Histone_H3]-lysine(36)_N-dimethyltransferase [Histone H3]-lysine(36) N-dimethyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.357 2.1.1.357] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Wolf-Hirschhorn syndrome. A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH. WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.	+	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Wolf-Hirschhorn syndrome. A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH. WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Histone methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.<ref>PMID:11152655</ref> <ref>PMID:16115125</ref> <ref>PMID:18172012</ref>	+	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Histone methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.<ref>PMID:11152655</ref> <ref>PMID:16115125</ref> <ref>PMID:18172012</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao~~, D Y~~]]	+	[[Category: Cao DY]]
-	[[Category: Li, J]]	+	[[Category: Li J]]
-	[[Category: Li~~, Y L~~]]	+	[[Category: Li YL]]
-	[[Category: Xiong, B]]	+	[[Category: Xiong B]]
-	~~[[Category: Histone-lysine n-methyltransferase nsd2]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:28, 13 July 2022

OCA — Wed, 13 Jul 2022 05:28:35 GMT

←Older revision		Revision as of 05:28, 13 July 2022
Line 1:		Line 1:

	==NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound==		==NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound==
-	<StructureSection load='7vln' size='340' side='right'caption='[[7vln]]' scene=''>	+	<StructureSection load='7vln' size='340' side='right'caption='[[7vln]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vln]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QC:4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile'>7QC</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Histone_H3]-lysine(36)_N-dimethyltransferase [Histone H3]-lysine(36) N-dimethyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.357 2.1.1.357] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Wolf-Hirschhorn syndrome. A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH. WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/NSD2_HUMAN NSD2_HUMAN]] Histone methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. Isoform 2 may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.<ref>PMID:11152655</ref> <ref>PMID:16115125</ref> <ref>PMID:18172012</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Overexpression, point mutations, or translocations of protein lysine methyltransferase NSD2 occur in many types of cancer cells. Therefore, it was recognized as onco-protein and considered as a promising anticancer drug target. NSD2 consists of multiple domains including a SET catalytic domain and two PWWP domains binding to methylated histone proteins. Here, we reported our efforts to develop a series of NSD2-PWWP1 inhibitors, and further structure-based optimization resulted in a potent inhibitor 38, which has high selectivity toward the NSD2-PWWP1 domain. The detailed biological evaluation revealed that compound 38 can bind to NSD2-PWWP1 and then affect the expression of genes regulated by NSD2. The current discovery will provide a useful chemical probe to the future research in understanding the specific regulation mode of NSD2 by PWWP1 recognition and pave the way to develop potential drugs targeting NSD2 protein.
		+
		+	Structure-Based Discovery of a Series of NSD2-PWWP1 Inhibitors.,Li N, Yang H, Liu K, Zhou L, Huang Y, Cao D, Li Y, Sun Y, Yu A, Du Z, Yu F, Zhang Y, Wang B, Geng M, Li J, Xiong B, Xu S, Huang X, Liu T J Med Chem. 2022 Jun 15. doi: 10.1021/acs.jmedchem.2c00709. PMID:35704853<ref>PMID:35704853</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vln" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao DY]]	+	[[Category: Cao, D Y]]
-	[[Category: Li J]]	+	[[Category: Li, J]]
-	[[Category: Li YL]]	+	[[Category: Li, Y L]]
-	[[Category: Xiong B]]	+	[[Category: Xiong, B]]
		+	[[Category: Histone-lysine n-methyltransferase nsd2]]
		+	[[Category: Transferase]]

OCA at 16:15, 6 July 2022

OCA — Wed, 06 Jul 2022 16:15:20 GMT

←Older revision		Revision as of 16:15, 6 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7vln is ON HOLD until 2023~~-10-05	+	==NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound==
-		+	<StructureSection load='7vln' size='340' side='right'caption='[[7vln]]' scene=''>
-	~~Authors~~: ~~Cao~~, D.Y., Li, Y.L., ~~Li, J~~., ~~Xiong, B~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VLN FirstGlance]. <br>
-	~~Description: NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vln OCA], [https://pdbe.org/7vln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vln RCSB], [https://www.ebi.ac.uk/pdbsum/7vln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vln ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Cao~~, D.Y~~]]	+	__TOC__
-	[[Category: Li, J]]	+	</StructureSection>
-	[[Category: Li~~, Y.L~~]]	+	[[Category: Large Structures]]
-	[[Category: Xiong, B]]	+	[[Category: Cao DY]]
		+	[[Category: Li J]]
		+	[[Category: Li YL]]
		+	[[Category: Xiong B]]

OCA at 06:50, 22 June 2022

OCA — Wed, 22 Jun 2022 06:50:25 GMT

←Older revision		Revision as of 06:50, 22 June 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vln is ON HOLD until ~~Oct 05~~ 2023	+	The entry 7vln is ON HOLD until 2023-10-05

	Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B.		Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Cao, D.Y]]		[[Category: Cao, D.Y]]
-	[[Category: Xiong, B]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Li, Y.L]]		[[Category: Li, Y.L]]
		+	[[Category: Xiong, B]]

OCA at 14:11, 22 December 2021

OCA — Wed, 22 Dec 2021 14:11:50 GMT

←Older revision		Revision as of 14:11, 22 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vln is ON HOLD	+	The entry 7vln is ON HOLD until Oct 05 2023

	Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B.		Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Cao, D.Y]]		[[Category: Cao, D.Y]]
		+	[[Category: Xiong, B]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Li, Y.L]]		[[Category: Li, Y.L]]
-	[[Category: Xiong, B]]

OCA: Protected "7vln" [edit=sysop:move=sysop]

OCA — Wed, 13 Oct 2021 10:34:13 GMT

Protected "7vln" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 13 October 2021

OCA: New page: '''Unreleased structure''' The entry 7vln is ON HOLD Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B. Description: NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound [[...

OCA — Wed, 13 Oct 2021 10:34:11 GMT

New page: '''Unreleased structure''' The entry 7vln is ON HOLD Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B. Description: NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound [[...

New page

'''Unreleased structure'''

The entry 7vln is ON HOLD

Authors: Cao, D.Y., Li, Y.L., Li, J., Xiong, B.

Description: NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound
[[Category: Unreleased Structures]]
[[Category: Cao, D.Y]]
[[Category: Li, J]]
[[Category: Li, Y.L]]
[[Category: Xiong, B]]