[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

TitleRoom-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B.
Journal, issue, pagesElife, Vol. 12, Year 2023
Publish dateOct 19, 2022 (structure data deposition date)
AuthorsSkaist Mehlman, T. / Biel, J.T. / Azeem, S.M. / Nelson, E.R. / Hossain, S. / Dunnett, L. / Paterson, N.G. / Douangamath, A. / Talon, R. / Axford, D. ...Skaist Mehlman, T. / Biel, J.T. / Azeem, S.M. / Nelson, E.R. / Hossain, S. / Dunnett, L. / Paterson, N.G. / Douangamath, A. / Talon, R. / Axford, D. / Orins, H. / von Delft, F. / Keedy, D.A.
External linksElife / PubMed:36881464
MethodsX-ray diffraction
Resolution1.77 - 2.54 Å
Structure data

PDB-7fqm:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000619a
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7fqn:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000497a
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7fqo:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000523a
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-7fqp:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000505a
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7fqq:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000611a
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7fqr:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000666a
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7fqs:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000555a
Method: X-RAY DIFFRACTION / Resolution: 2.12 Å

PDB-7fqt:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000293a
Method: X-RAY DIFFRACTION / Resolution: 2.54 Å

PDB-7fqu:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000470b
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7fqv:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000847b
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7fqw:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOCR000171b
Method: X-RAY DIFFRACTION / Resolution: 2.17 Å

PDB-7fqx:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000601a
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

PDB-7fqy:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000278a
Method: X-RAY DIFFRACTION / Resolution: 2.13 Å

PDB-7fqz:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000203a
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-7fre:
PanDDA analysis group deposition -- Crystal structure of PTP1B after initial refinement with no ligand modeled
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7frf:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000089a
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-7frg:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z31222641
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7frh:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434762
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7fri:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z321318226
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7frj:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434770
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7frk:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z30820160
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7frl:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434917
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-7frm:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z509756472
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7frn:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z915492990
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7fro:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z744754722
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-7frp:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000245b
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7frq:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000217b
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-7frr:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434906
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-7frs:
PanDDA analysis group deposition of ground-state model of PTP1B
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-7frt:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster 1
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7fru:
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster 2
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

Chemicals

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-JKG:
4-({[(thiophen-2-yl)methyl]amino}methyl)phenol

ChemComp-HOH:
WATER / Water

ChemComp-JKA:
(1S,4R,5S,6R)-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane-4,6-diol

ChemComp-WUW:
(1R,4R,5R,6S)-2-(methanesulfonyl)-4,6-dimethoxy-2-azabicyclo[3.3.1]nonane

ChemComp-JN1:
(6R)-5,6-dihydro-1H-2,6-methano-1lambda~6~-1lambda~6~,2,5-benzothiadiazocine-1,1,4(3H)-trione

ChemComp-JKJ:
(1R,3R,4S)-3-(methoxymethyl)-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-ol

ChemComp-JPD:
methyl (1S,3S,4R)-4-hydroxy-3-[(1S)-1-hydroxypropyl]-2-azabicyclo[2.2.2]octane-2-carboxylate

ChemComp-JPV:
(2R,5R,6S)-2,3,4,5,6,7-hexahydro-1H-2,6-methanoazocino[5,4-b]indol-5-ol

ChemComp-JJY:
3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione

ChemComp-JMV:
(3-chlorophenoxy)acetic acid

ChemComp-JGD:
N,N-dimethylpyridin-4-amine / 4-Dimethylaminopyridine

ChemComp-JG4:
2-(thiophen-2-yl)-1H-imidazole

ChemComp-JHD:
1-(3,4-dimethoxyphenyl)methanamine

ChemComp-GRY:
~{N}1-(4,6-dimethylpyrimidin-2-yl)benzene-1,4-diamine

ChemComp-WV0:
5-fluoro-1,3-dihydro-2H-indol-2-one

ChemComp-6SU:
methyl 3-(methylsulfonylamino)benzoate

ChemComp-GV1:
~{N},~{N},5,6-tetramethylthieno[2,3-d]pyrimidin-4-amine

ChemComp-JHJ:
N-(4-methoxyphenyl)-N'-pyridin-4-ylurea

ChemComp-JFJ:
1-(3-chlorophenyl)-N-methylmethanamine

ChemComp-JFP:
N-(4-methyl-1,3-thiazol-2-yl)propanamide

ChemComp-JGG:
N-[(4-cyanophenyl)methyl]morpholine-4-carboxamide

ChemComp-JO1:
1-methyl-N-[(thiophen-2-yl)methyl]-1H-pyrazole-5-carboxamide

ChemComp-JL4:
5-(2-methyl-1,3-thiazol-4-yl)thiophene-2-carboxylic acid

ChemComp-JLG:
2-(thiophen-2-yl)-1,3-thiazole-4-carboxylic acid

ChemComp-O1J:
(benzyloxy)acetic acid

Source
  • homo sapiens (human)
KeywordsHYDROLASE / PanDDA / Diamond i24 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer

+
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://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