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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

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

ChemComp-HOH:
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

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

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