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Structure paper

TitleAn expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data.
Journal, issue, pagesBiorxiv, Year 2024
Publish dateJan 3, 2024 (structure data deposition date)
AuthorsMehlman, T.S. / Ginn, H.M. / Keedy, D.A.
External linksBiorxiv / PubMed:38260327
MethodsX-ray diffraction
Resolution1.59 - 2.47 Å
Structure data

PDB-7gs7:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000621a
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gs8:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000466a
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7gs9:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000631a
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-7gsa:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000260a
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7gsb:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000438a
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7gsc:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000729a
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7gsd:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000605a
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7gse:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000383a
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-7gsf:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000421a
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7gsg:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000316a
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7gsh:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000530a
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-7gsi:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000046b
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7gsj:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000543a
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7gsk:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000279a
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7gsl:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000274b
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7gsm:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000437b
Method: X-RAY DIFFRACTION / Resolution: 2.03 Å

PDB-7gsn:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000519b
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-7gso:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000029a
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7gsq:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000149a
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7gsr:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000055b
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7gst:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000056a
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-7gsu:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000382a
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7gsv:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000830b
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-7gsw:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000422b
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-7gsx:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001440b
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7gsy:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001175b
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7gsz:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000686b
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7gt0:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000275a
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7gt1:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000209a
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7gt2:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000752b
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7gt3:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000527a
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7gt4:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000528a
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7gt5:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000529a
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-7gt6:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000530a
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gt7:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001181b
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-7gt8:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001439b
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7gt9:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000463b
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7gta:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000065a
Method: X-RAY DIFFRACTION / Resolution: 2.06 Å

PDB-7gtb:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000899b
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7gtc:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00001145b
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-7gtd:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000110a
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7gte:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000646b
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7gtf:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000754b
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7gtg:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000684a
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-7gth:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000637a
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gti:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000571a
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gtj:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000280c
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-7gtk:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000552a
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7gtl:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000554a
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-7gtm:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000543a
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-7gtn:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000625a
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7gto:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000602a
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7gtp:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000688a
Method: X-RAY DIFFRACTION / Resolution: 2.47 Å

PDB-7gtq:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000311a
Method: X-RAY DIFFRACTION / Resolution: 2.09 Å

PDB-7gtr:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000587a
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7gts:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000604a
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7gtt:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000148a
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-7gtu:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000297a
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-7gtv:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000765c
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

Chemicals

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

ChemComp-RU4:
4-(1,2,3-thiadiazol-4-yl)phenyl ethylcarbamate

ChemComp-HOH:
WATER / Water

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

ChemComp-LV7:
~{N}-[2-(aminocarbamoyl)phenyl]ethanamide

PDB-1aa6:
REDUCED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI

PDB-1aa7:
INFLUENZA VIRUS MATRIX PROTEIN CRYSTAL STRUCTURE AT PH 4.0

ChemComp-WLJ:
(azepan-1-yl)(2,6-difluorophenyl)methanone

ChemComp-GVY:
4-(5-amino-1,3,4-thiadiazol-2-yl)phenol

ChemComp-T1J:
2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol

ChemComp-B0Y:
5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide

ChemComp-RZG:
methyl 4-sulfamoylbenzoate

ChemComp-WLY:
2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide

ChemComp-LWV:
2-morpholin-4-ylaniline

ChemComp-B0G:
(phenylmethyl) 4-oxidanylpiperidine-1-carboxylate

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol


PDB Unreleased entry

PDB-1aa8: Unknown entry

PDB-1abb:
CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: CRYSTALLOGRAPHIC STUDIES ON R-STATE GLYCOGEN PHOSPHORYLASE RECONSTITUTED WITH PYRIDOXAL 5'-DIPHOSPHATE

ChemComp-R7T:
4-[(thiophen-2-yl)methyl]benzoic acid

PDB-1aba:
THE STRUCTURE OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN (THIOREDOXIN). REFINEMENT OF NATIVE AND MUTANT PROTEINS

ChemComp-JKY:
N-[(4-chlorophenyl)methyl]methanesulfonamide

PDB-1aa9:
HUMAN C-HA-RAS(1-171)(DOT)GDP, NMR, MINIMIZED AVERAGE STRUCTURE

PDB-1abc:
Unknown entry

ChemComp-I8M:
2-[(morpholin-4-yl)methyl]phenol

PDB-1abd:
Unknown entry

PDB-1abe:
NOVEL STEREOSPECIFICITY OF THE L-ARABINOSE-BINDING PROTEIN

ChemComp-JLM:
3-methyl-1-benzofuran-2-carboxylic acid

PDB-1abf:
SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES

ChemComp-WFI:
1-[4-methyl-2-(pyridin-4-yl)-1,3-thiazol-5-yl]methanamine

PDB-1abg:
Unknown entry


PDB Unreleased entry

PDB-1abh: Unknown entry

ChemComp-JNG:
[(4-chlorophenyl)sulfanyl]acetic acid

PDB-1abi:
STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS

PDB-1abj:
STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS


PDB Unreleased entry

PDB-1abk: Unknown entry


PDB Unreleased entry

PDB-1ack: Unknown entry

PDB-1abl:
Unknown entry

ChemComp-8K2:
5-chloranylthiophene-2-sulfonamide

PDB-1abr:
CRYSTAL STRUCTURE OF ABRIN-A

PDB-1abq:
CRYSTAL STRUCTURE OF THE UNLIGANDED ABL TYROSINE KINASE SH3 DOMAIN

ChemComp-4ZV:
1H-indole-5-carboxylic acid

ChemComp-LVD:
1-phenylmethoxyurea


PDB Unreleased entry

PDB-1abp: Unknown entry

PDB-1abo:
CRYSTAL STRUCTURE OF THE COMPLEX OF THE ABL TYROSINE KINASE SH3 DOMAIN WITH 3BP-1 SYNTHETIC PEPTIDE

ChemComp-9EW:
1,2-benzoxazol-3-ol

PDB-1abn:
THE CRYSTAL STRUCTURE OF THE ALDOSE REDUCTASE NADPH BINARY COMPLEX


PDB Unreleased entry

PDB-1abm: Unknown entry

PDB-1aby:
CYANOMET RHB1.1 (RECOMBINANT HEMOGLOBIN)

ChemComp-JP4:
[2-(morpholin-4-yl)phenyl]methanol


PDB Unreleased entry

PDB-1abx: Unknown entry

PDB-1abw:
DEOXY RHB1.1 (RECOMBINANT HEMOGLOBIN)

PDB-1abv:
N-TERMINAL DOMAIN OF THE DELTA SUBUNIT OF THE F1F0-ATP SYNTHASE FROM ESCHERICHIA COLI, NMR, MINIMIZED AVERAGE STRUCTURE

PDB-1abu:
Unknown entry

PDB-1abt:
NMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN(SLASH)NICOTINIC RECEPTOR PEPTIDE COMPLEX

ChemComp-W1D:
(4-acetylphenoxy)acetic acid

ChemComp-S7S:
~{N}-(2-ethyl-1,2,3,4-tetrazol-5-yl)butanamide

ChemComp-TAH:
2-(benzyloxy)benzohydrazide

ChemComp-WZY:
N-(4-methoxyphenyl)glycinamide

PDB-1abs:
PHOTOLYSED CARBONMONOXY-MYOGLOBIN AT 20 K

ChemComp-8YM:
2-[(2-acetylphenyl)sulfanyl]benzoic acid

ChemComp-UJQ:
9~{H}-xanthene-9-carboxylic acid

Source
  • homo sapiens (human)
KeywordsHYDROLASE / PanDDA / Diamond I04-1 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer

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