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5B0U
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CRYSTAL STRUCTURE OF THE MUTATED 19 KDA PROTEIN OF OPLOPHORUS LUCIFERASE (NANOKAZ)
Descriptor:Oplophorus-luciferin 2-monooxygenase catalytic subunit
Authors:Tomabechi, Y., Ehara, H., Sekine, S.I., Shirouzu, M.
Deposit date:2015-11-04
Release date:2016-01-13
Last modified:2016-02-10
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine
Biochem.Biophys.Res.Commun., 470, 2016
5H09
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR (S)-ETHYL2-(((1R,4S)-4-(4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)CYCLOHEXYL)AMINO)-4-METHYLPENTANOATE
Descriptor:Tyrosine-protein kinase HCK, ethyl (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-4-methyl-pentanoate
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-10-04
Release date:2017-10-04
Method:X-RAY DIFFRACTION (1.945 Å)
Cite:Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Bioorg. Med. Chem., 25, 2017
5H0B
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR (S)-2-(((1R,4S)-4-(4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)CYCLOHEXYL)AMINO)-4-METHYLPENTANOIC ACID
Descriptor:Tyrosine-protein kinase HCK, (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]azaniumyl]-4-methyl-pentanoate
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-10-04
Release date:2017-10-11
Method:X-RAY DIFFRACTION (1.651 Å)
Cite:Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Bioorg. Med. Chem., 25, 2017
5H0E
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR (S)-2-(((1R,4S)-4-(4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)CYCLOHEXYL)AMINO)-4-METHYLPENTANAMIDE
Descriptor:Tyrosine-protein kinase HCK, (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-4-methyl-pentanamide
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-10-04
Release date:2017-10-04
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Bioorg. Med. Chem., 25, 2017
5H0G
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR (S)-2-(((1R,4S)-4-(4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)CYCLOHEXYL)AMINO)-N,4-DIMETHYLPENTANAMIDE
Descriptor:Tyrosine-protein kinase HCK, (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},4-dimethyl-pentanamide
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-10-04
Release date:2017-10-04
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Bioorg. Med. Chem., 25, 2017
5H0H
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR (S)-2-(((1R,4S)-4-(4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)CYCLOHEXYL)AMINO)-N,N,4-TRIMETHYLPENTANAMIDE
Descriptor:Tyrosine-protein kinase HCK, (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},~{N},4-trimethyl-pentanamide
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-10-04
Release date:2017-10-04
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:Activity cliff for 7-substituted pyrrolo-pyrimidine inhibitors of HCK explained in terms of predicted basicity of the amine nitrogen.
Bioorg. Med. Chem., 25, 2017
5GV0
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CRYSTAL STRUCTURE OF THE MEMBRANE-PROXIMAL DOMAIN OF MOUSE LYSOSOME-ASSOCIATED MEMBRANE PROTEIN 1 (LAMP-1)
Descriptor:Lysosome-associated membrane glycoprotein 1, SULFATE ION, N-ACETYL-D-GLUCOSAMINE
Authors:Tomabechi, Y., Ehara, H., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-09-01
Release date:2016-10-12
Last modified:2016-10-19
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes
Biochem.Biophys.Res.Commun., 479, 2016
5GV3
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CRYSTAL STRUCTURE OF THE MEMBRANE-DISTAL DOMAIN OF MOUSE LYSOSOME-ASSOCIATED MEMBRANE PROTEIN 2 (LAMP-2)
Descriptor:Lysosome-associated membrane glycoprotein 2, ZINC ION, N-ACETYL-D-GLUCOSAMINE
Authors:Tomabechi, Y., Ehara, H., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2016-09-01
Release date:2017-09-06
Last modified:2019-03-20
Method:X-RAY DIFFRACTION (2.096 Å)
Cite:Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes.
Biochem. Biophys. Res. Commun., 479, 2016
5ZJ6
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CRYSTAL STRUCTURE OF HCK KINASE COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 7-[TRANS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
Descriptor:Tyrosine-protein kinase HCK, 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
Authors:Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.
Deposit date:2018-03-19
Release date:2018-06-06
Last modified:2018-06-13
Method:X-RAY DIFFRACTION (1.696 Å)
Cite:Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression.
Protein Expr. Purif., 150, 2018
3VRY
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 4-AMINO-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL-CYCLOPENTANE
Descriptor:Tyrosine-protein kinase HCK, 4-Amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl-cyclopentane, CHLORIDE ION, ...
Authors:Kuratani, M., Tomabechi, Y., Niwa, H., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.481 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VRZ
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)PHENYL]-3-BENZYLUREA
Descriptor:Tyrosine-protein kinase HCK, CALCIUM ION, CHLORIDE ION, ...
Authors:Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.218 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS0
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR N-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)PHENYL]BENZAMIDE
Descriptor:Tyrosine-protein kinase HCK, CALCIUM ION, CHLORIDE ION, ...
Authors:Kuratani, M., Honda, K., Tomabechi, Y., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.934 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS1
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)PHENYL]-3-PHENYLUREA
Descriptor:Tyrosine-protein kinase HCK, CALCIUM ION, CHLORIDE ION, ...
Authors:Kuratani, M., Tomabechi, Y., Toyama, M., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.464 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS2
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 7-[CIS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
Descriptor:Tyrosine-protein kinase HCK, 7-[cis-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine, CALCIUM ION, ...
Authors:Kuratani, M., Tomabechi, Y., Niwa, H., Parker, J.L., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.609 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS4
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 5-(4-PHENOXYPHENYL)-7-(TETRAHYDRO-2H-PYRAN-4-YL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
Descriptor:Tyrosine-protein kinase HCK, CALCIUM ION, CHLORIDE ION, ...
Authors:Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.747 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS5
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 7-(1-METHYLPIPERIDIN-4-YL)-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
Descriptor:Tyrosine-protein kinase HCK, 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine, CALCIUM ION
Authors:Kuratani, M., Tomabechi, Y., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.851 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3VS6
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CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRAZOLO-PYRIMIDINE INHIBITOR TERT-BUTYL {4-[4-AMINO-1-(PROPAN-2-YL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL]-2-METHOXYPHENYL}CARBAMATE
Descriptor:Tyrosine-protein kinase HCK, CALCIUM ION, CHLORIDE ION, ...
Authors:Kuratani, M., Honda, K., Tomabechi, Y., Toyama, M., Handa, N., Yokoyama, S.
Deposit date:2012-04-21
Release date:2013-05-01
Method:X-RAY DIFFRACTION (2.373 Å)
Cite:A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo
Sci Transl Med, 5, 2013
3QHE
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CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE ARMADILLO REPEAT DOMAIN OF ADENOMATOUS POLYPOSIS COLI AND THE TYROSINE-RICH DOMAIN OF SAM68
Descriptor:Adenomatous polyposis coli protein, KH domain-containing, RNA-binding, ...
Authors:Morishita, E.C.J., Murayama, K., Kato-Murayama, M., Ishizuku-Katsura, Y., Tomabechi, Y., Terada, T., Handa, N., Shirouzu, M., Akiyama, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2011-01-25
Release date:2011-11-02
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structures of the armadillo repeat domain of adenomatous polyposis coli and its complex with the tyrosine-rich domain of sam68
Structure, 19, 2011
5X1A
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CRYSTAL STRUCTURE OF HUMAN CRMP-2
Descriptor:Dihydropyrimidinase-related protein 2
Authors:Nitta, R., Tomabechi, Y., Aoki, M., Shirouzu, M.
Deposit date:2017-01-25
Release date:2017-09-20
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (1.821 Å)
Cite:Structural basis for CRMP2-induced axonal microtubule formation
Sci Rep, 7, 2017
5X1C
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CRYSTAL STRUCTURE OF HUMAN CRMP-2 WITHOUT C-TERMINAL TAIL
Descriptor:Dihydropyrimidinase-related protein 2
Authors:Nitta, R., Tomabechi, Y., Aoki, M., Shirouzu, M.
Deposit date:2017-01-25
Release date:2017-09-20
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (2.101 Å)
Cite:Structural basis for CRMP2-induced axonal microtubule formation
Sci Rep, 7, 2017
5X1D
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CRYSTAL STRUCTURE OF T246A-N247A HUMAN CRMP-2 MUTANT
Descriptor:Dihydropyrimidinase-related protein 2
Authors:Nitta, R., Tomabechi, Y., Aoki, M., Shirouzu, M.
Deposit date:2017-01-25
Release date:2017-09-20
Last modified:2017-09-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for CRMP2-induced axonal microtubule formation
Sci Rep, 7, 2017
3VUZ
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CRYSTAL STRUCTURE OF HISTONE METHYLTRANSFERASE SET7/9 IN COMPLEX WITH AAM-1
Descriptor:Histone-lysine N-methyltransferase SETD7, 5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine
Authors:Niwa, H., Handa, N., Tomabechi, Y., Honda, K., Toyama, M., Ohsawa, N., Shirouzu, M., Kagechika, H., Hirano, T., Umehara, T., Yokoyama, S.
Deposit date:2012-07-10
Release date:2013-03-27
Last modified:2016-09-28
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives
Acta Crystallogr.,Sect.D, 69, 2013
3VV0
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CRYSTAL STRUCTURE OF HISTONE METHYLTRANSFERASE SET7/9 IN COMPLEX WITH DAAM-3
Descriptor:Histone-lysine N-methyltransferase SETD7, 5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine
Authors:Niwa, H., Handa, N., Tomabechi, Y., Honda, K., Toyama, M., Ohsawa, N., Shirouzu, M., Kagechika, H., Hirano, T., Umehara, T., Yokoyama, S.
Deposit date:2012-07-10
Release date:2013-03-27
Last modified:2016-09-28
Method:X-RAY DIFFRACTION (2.001 Å)
Cite:Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives
Acta Crystallogr.,Sect.D, 69, 2013
4WR4
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CRYSTAL STRUCTURE OF GST MUTATED WITH HALOGENATED TYROSINE (7BGST-1)
Descriptor:Glutathione S-transferase class-mu 26 kDa isozyme, GLUTATHIONE, SULFATE ION
Authors:Akasaka, R., Kawazoe, M., Tomabechi, Y., Ohtake, K., Itagaki, T., Takemoto, C., Shirouzu, M., Yokoyama, S., Sakamoto, K.
Deposit date:2014-10-23
Release date:2015-08-19
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
4WR5
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CRYSTAL STRUCTURE OF GST MUTATED WITH HALOGENATED TYROSINE (7CGST-1)
Descriptor:Glutathione S-transferase class-mu 26 kDa isozyme, GLUTATHIONE, SULFATE ION
Authors:Akasaka, R., Kawazoe, M., Tomabechi, Y., Ohtake, K., Itagaki, T., Takemoto, C., Shirouzu, M., Yokoyama, S., Sakamoto, K.
Deposit date:2014-10-23
Release date:2015-08-19
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Protein stabilization utilizing a redefined codon
Sci Rep, 5, 2015
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