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PDB: 61 results

6RRH
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GOLGI ALPHA-MANNOSIDASE II
Descriptor: 1,2-ETHANEDIOL, Alpha-mannosidase 2, ZINC ION
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-18
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RRW
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GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol
Descriptor: (2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol, Alpha-mannosidase 2, ZINC ION
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
7NL5
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Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor
Descriptor: (1R,2R,3R,4S,5R)-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol, (1R,6S)-5beta-(Hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2beta,3beta,4alpha-triol, Alpha-1,6-mannanase, ...
Authors:Schroeder, S, Offen, W.A, Males, A, Jin, Y, De Boer, C, Enotarpi, J, Marino, L, van der Marel, G.A, Florea, B.I, Codee, J.D.C, Overkleeft, H.S, Davies, G.J.
Deposit date:2021-02-22
Release date:2021-04-28
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on alpha-1,6 Mannanases.
Chemistry, 27, 2021
6RRX
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GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-3-piperidinol
Descriptor: (2~{S},3~{R})-2-(hydroxymethyl)piperidin-3-ol, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RRJ
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GOLGI ALPHA-MANNOSIDASE II in complex with 5-(Adamantan-1yl-methoxy)-pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide
Descriptor: (2~{S},3~{R},4~{S},5~{R})-~{N}-[5-(1-adamantylmethoxy)pentyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidine-2-carboxamide, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RRU
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GOLGI ALPHA-MANNOSIDASE II in complex with (5R,6R,7S,8S)-5,6,7,8-tetrahydro-5-(hydroxymethyl)-3-(3-phenylpropyl)imidazo[1,2-a]pyridine-6,7,8-triol
Descriptor: (5~{R},6~{R},7~{S},8~{S})-5-(hydroxymethyl)-2-(3-phenylpropyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-6,7,8-triol, Alpha-mannosidase 2, ZINC ION
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RRN
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GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide
Descriptor: (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RRY
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GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol
Descriptor: (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
6RS0
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GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3S,4R,5R)-1-(2-(Benzyloxy)ethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol
Descriptor: (2~{S},3~{S},4~{R})-2-(hydroxymethyl)-1-(2-phenylmethoxyethyl)piperidine-3,4,5-triol, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-20
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
1KYI
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HslUV (H. influenzae)-NLVS Vinyl Sulfone Inhibitor Complex
Descriptor: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE, ADENOSINE-5'-TRIPHOSPHATE, ATP-dependent hsl protease ATP-binding subunit hslU, ...
Authors:Sousa, M.C, Kessler, B.M, Overkleeft, H.S, McKay, D.B.
Deposit date:2002-02-04
Release date:2002-05-15
Last modified:2023-08-16
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Crystal Structure of HslUV Complexed with a Vinyl Sulfone Inhibitor: Corroboration of a Proposed Mechanism of Allosteric Activation of HslV by HslU
J.Mol.Biol., 318, 2002
1OFI
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Asymmetric complex between HslV and I-domain deleted HslU (H. influenzae)
Descriptor: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE, ADENOSINE-5'-DIPHOSPHATE, ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU, ...
Authors:Kwon, A.R, Kessler, B.M, Overkleeft, H.S, McKay, D.B.
Deposit date:2003-04-14
Release date:2003-07-03
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structure and Reactivity of an Asymmetric Complex between Hslv and I-Domain Deleted Hslu, a Prokaryotic Homolog of the Eukaryotic Proteasome
J.Mol.Biol., 330, 2003
1OFH
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Asymmetric complex between HslV and I-domain deleted HslU (H. influenzae)
Descriptor: ADENOSINE-5'-DIPHOSPHATE, ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU, ATP-DEPENDENT PROTEASE HSLV, ...
Authors:Kwon, A.R, Kessler, B.M, Overkleeft, H.S, McKay, D.B.
Deposit date:2003-04-14
Release date:2003-07-03
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure and Reactivity of an Asymmetric Complex between Hslv and I-Domain Deleted Hslu, a Prokaryotic Homolog of the Eukaryotic Proteasome
J.Mol.Biol., 330, 2003
5OSS
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Beta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole
Descriptor: (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol, 1,2-ETHANEDIOL, Beta-glucosidase A, ...
Authors:Offen, W.A, Schroeder, S.P, Davies, G.J, Overkleeft, H.S.
Deposit date:2017-08-18
Release date:2018-04-11
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor.
J. Am. Chem. Soc., 140, 2018
8CQI
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Human heparanase in complex with inhibitor R3794
Descriptor: (3~{S},4~{S})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid, 1,2-ETHANEDIOL, 1,5-anhydro-D-arabinitol, ...
Authors:Moran, E.M, Davies, G.J, Chen, C, Nieuwendijk, E.V, Wu, L, Skoulikopoulou, F, Riet, V.V, Overkleeft, H.S, Armstrong, Z.
Deposit date:2023-03-06
Release date:2024-01-10
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B.
J.Am.Chem.Soc., 146, 2024
8CB1
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Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-PNT-DNM 15
Descriptor: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-[5-(phenanthren-9-ylmethoxy)pentyl]piperidine-3,4,5-triol, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Sulzenbacher, G, Roig-Zamboni, V, Overkleeft, H, Artola, M.
Deposit date:2023-01-25
Release date:2023-09-13
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases.
Chem Sci, 14, 2023
8CB6
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Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in covalent complex with TAMRA tagged 1,6-Epi-cylcophellitol aziridine activity based probe
Descriptor: (1S,2R,3R,4R,5R)-5-[8-[4-(4-azanylbutyl)-1,2,3-triazol-1-yl]octylamino]-4-(hydroxymethyl)cyclohexane-1,2,3-triol, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Sulzenbacher, G, Roig-Zamboni, V, Overkleeft, H, Artola, M.
Deposit date:2023-01-25
Release date:2023-09-13
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases.
Chem Sci, 14, 2023
9FT0
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Yeast 20S proteasome in complex with epoxyketone inhibitor 42
Descriptor: (2S)-N-[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-3-(4-methoxyphenyl)-1-oxidanylidene-propan-2-yl]-2-(2-morpholin-4-ylethanoylamino)-4-oxidanyl-butanamide, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, ...
Authors:Maurits, E, Huber, E.M, Dekker, P.M, Wang, X, Heinemeyer, W, Florea, B.I, Groll, M, Overkleeft, H.S.
Deposit date:2024-06-23
Release date:2024-07-10
Last modified:2024-07-17
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites
to be published
9FT1
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Yeast 20S proteasome in complex with epoxyketone inhibitor 13
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, MAGNESIUM ION, Probable proteasome subunit alpha type-7, ...
Authors:Maurits, E, Huber, E.M, Dekker, P.M, Wang, X, Heinemeyer, W, Florea, B.I, Groll, M, Overkleeft, H.S.
Deposit date:2024-06-23
Release date:2024-07-10
Last modified:2024-07-17
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites
to be published
9FST
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BU of 9fst by Molmil
Yeast 20S proteasome with human beta1i (1-51) in complex with epoxyketone inhibitor LU-001i
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, MAGNESIUM ION, ...
Authors:Maurits, E, Huber, E.M, Dekker, P.M, Wang, X, Heinemeyer, W, Florea, B.I, Groll, M, Overkleeft, H.S.
Deposit date:2024-06-21
Release date:2024-07-17
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites
To Be Published
9FSV
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Yeast 20S proteasome with human beta2i (1-53) in complex with epoxyketone inhibitor 42
Descriptor: (2S)-N-[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-3-(4-methoxyphenyl)-1-oxidanylidene-propan-2-yl]-2-(2-morpholin-4-ylethanoylamino)-4-oxidanyl-butanamide, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, ...
Authors:Maurits, E, Huber, E.M, Dekker, P.M, Wang, X, Heinemeyer, W, Florea, B.I, Groll, M, Overkleeft, H.S.
Deposit date:2024-06-22
Release date:2024-07-17
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites
to be published
7BZL
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GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol
Descriptor: (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol, Non-reducing end beta-L-arabinofuranosidase, ZINC ION
Authors:Amaki, S, McGregor, N.G.S, Arakawa, T, Yamada, C, Borlandelli, V, Overkleeft, H.S, Davies, G.J, Fushinobu, S.
Deposit date:2020-04-28
Release date:2021-01-27
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Angew.Chem.Int.Ed.Engl., 60, 2021
7DIF
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GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution
Descriptor: (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol, Non-reducing end beta-L-arabinofuranosidase, POTASSIUM ION, ...
Authors:Amaki, S, McGregor, N.G.S, Arakawa, T, Yamada, C, Borlandelli, V, Overkleeft, H.S, Davies, G.J, Fushinobu, S.
Deposit date:2020-11-19
Release date:2021-01-27
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Angew.Chem.Int.Ed.Engl., 60, 2021
6RQZ
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GOLGI ALPHA-MANNOSIDASE II complex with Manno-epi-cyclophellitol aziridine
Descriptor: (1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ...
Authors:Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, Debets, M, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J.
Deposit date:2019-05-16
Release date:2020-07-08
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.53 Å)
Cite:Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
J.Am.Chem.Soc., 142, 2020
4INR
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Yeast 20S proteasome in complex with the vinyl sulfone LU102
Descriptor: N3Phe-Leu-Leu-Phe(4-NH2CH2)-methyl vinyl sulfone, bound form, Proteasome component C1, ...
Authors:Geurink, P.P, van der Linden, W.A, Mirabella, A.C, Gallastegui, N, de Bruin, G, Blom, A.E.M, Voges, M.J, Mock, E.D, Florea, B.I, van der Marel, G.A, Driessen, C, van der Stelt, M, Groll, M, Overkleeft, H.S, Kisselev, A.F.
Deposit date:2013-01-06
Release date:2013-01-30
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Incorporation of Non-natural Amino Acids Improves Cell Permeability and Potency of Specific Inhibitors of Proteasome Trypsin-like Sites.
J.Med.Chem., 56, 2013
4INT
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Yeast 20S proteasome in complex with the vinyl sulfone LU122
Descriptor: HMB-Val-Ser-Phe(4-NH2CH2)-methyl vinyl sulfone, bound form, Proteasome component C1, ...
Authors:Geurink, P.P, van der Linden, W.A, Mirabella, A.C, Gallastegui, N, de Bruin, G, Blom, A.E.M, Voges, M.J, Mock, E.D, Florea, B.I, van der Marel, G.A, Driessen, C, van der Stelt, M, Groll, M, Overkleeft, H.S, Kisselev, A.F.
Deposit date:2013-01-06
Release date:2013-01-30
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Incorporation of Non-natural Amino Acids Improves Cell Permeability and Potency of Specific Inhibitors of Proteasome Trypsin-like Sites.
J.Med.Chem., 56, 2013

 

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