Author results

6IQ5
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CRYSTAL STRUCTURE OF CYP1B1 AND INHIBITOR HAVING AZIDE GROUP
Descriptor:Cytochrome P450 1B1, PROTOPORPHYRIN IX CONTAINING FE, 2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one
Authors:Kubo, M., Yamamoto, K., Itoh, T.
Deposit date:2018-11-06
Release date:2019-01-30
Method:X-RAY DIFFRACTION (3.7 Å)
Cite:Design and synthesis of selective CYP1B1 inhibitor via dearomatization of alpha-naphthoflavone.
Bioorg. Med. Chem., 27, 2019
6BW6
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HUMAN GPT (DPAGT1) H129 VARIANT IN COMPLEX WITH TUNICAMYCIN
Descriptor:UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase, Tunicamycin, (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Authors:Yoo, J., Kuk, A.C.Y., Mashalidis, E.H., Lee, S.-Y.
Deposit date:2017-12-14
Release date:2018-02-21
Last modified:2018-03-21
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Nat. Struct. Mol. Biol., 25, 2018
6BW5
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HUMAN GPT (DPAGT1) IN COMPLEX WITH TUNICAMYCIN
Descriptor:UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase, Tunicamycin, (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Authors:Yoo, J., Kuk, A.C.Y., Mashalidis, E.H., Lee, S.-Y.
Deposit date:2017-12-14
Release date:2018-02-21
Last modified:2018-03-21
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Nat. Struct. Mol. Biol., 25, 2018
6AD9
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CRYSTAL STRUCTURE OF PPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH DIBENZOOXEPINE DERIVATIVE COMPOUND-9
Descriptor:Peroxisome proliferator-activated receptor gamma, 12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha, 3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one
Authors:Takahashi, Y., Suzuki, M., Yamamoto, K., Saito, J.
Deposit date:2018-07-31
Release date:2018-11-14
Last modified:2018-12-05
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Development of Dihydrodibenzooxepine Peroxisome Proliferator-Activated Receptor (PPAR) Gamma Ligands of a Novel Binding Mode as Anticancer Agents: Effective Mimicry of Chiral Structures by Olefinic E/ Z-Isomers.
J. Med. Chem., 61, 2018
5ZWI
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INTERACTION BETWEEN VITAMIN D RECEPTOR (VDR) AND A LIGAND HAVING A DIENONE GROUP
Descriptor:Vitamin D3 receptor, 13-meric peptide from DRIP205 NR2 BOX peptide, (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one
Authors:Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.
Deposit date:2018-05-15
Release date:2018-07-18
Last modified:2018-08-08
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5ZWH
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COVALENT BOND FORMATION BETWEEN HISTIDINE OF VITAMIN D RECEPTOR (VDR) AND A FULL AGONIST HAVING AN ENE-YNONE GROUP VIA CONJUGATE ADDITION REACTION
Descriptor:Vitamin D3 receptor, 13-meric peptide from DRIP205 NR2 BOX peptide, (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one, ...
Authors:Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.
Deposit date:2018-05-15
Release date:2018-07-18
Last modified:2018-08-08
Method:X-RAY DIFFRACTION (2.38 Å)
Cite:Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5ZWF
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COVALENT BOND FORMATION BETWEEN HISTIDINE OF VITAMIN D RECEPTOR (VDR) AND A FULL AGONIST HAVING A ENONE WITH A BETA METHYL GROUP VIA CONJUGATE ADDITION REACTION
Descriptor:Vitamin D3 receptor, 13-meric peptide from DRIP205 NR2 BOX peptide, (E,7R)-7-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one
Authors:Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.
Deposit date:2018-05-15
Release date:2018-07-18
Last modified:2018-08-08
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5ZWE
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COVALENT BOND FORMATION BETWEEN HISTIDINE OF VITAMIN D RECEPTOR (VDR) AND A FULL AGONIST HAVING A VINYL KETONE GROUP VIA CONJUGATE ADDITION REACTION
Descriptor:Vitamin D3 receptor, 13-meric peptide from DRIP205 NR2 BOX peptide, (6R)-6-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]hept-1-en-3-one
Authors:Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.
Deposit date:2018-05-15
Release date:2018-07-18
Last modified:2018-08-08
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem., 61, 2018
5ZFG
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CRYSTAL STRUCTURE OF A DIAZINON-METABOLIZING GLUTATHIONE S-TRANSFERASE IN THE SILKWORM, BOMBYX MORI
Descriptor:Glutathione S-transferase, 1,2-ETHANEDIOL, ACETATE ION
Authors:Yamamoto, K., Higashiura, A., Nakagawa, A.
Deposit date:2018-03-06
Release date:2018-09-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of a diazinon-metabolizing glutathione S-transferase in the silkworm, Bombyx mori
To Be Published
5ZF1
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MOLECULAR STRUCTURE OF A NOVEL 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE FROM THE SILKWORM, BOMBYX MORI
Descriptor:5,10-methylenetetrahydrofolate dehydrogenase, SULFATE ION, 1,2-ETHANEDIOL
Authors:Haque, R., Higashiura, A., Nakagawa, A., Yamamoto, K.
Deposit date:2018-03-02
Release date:2019-01-23
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Molecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from the silkworm, Bombyx mori
To Be Published
5ZEQ
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CARBOXYPEPTIDASE B IN COMPLEX WITH DD28
Descriptor:Carboxypeptidase B, ZINC ION, (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid, ...
Authors:Itoh, T., Yoshimoto, N., Yamamoto, K.
Deposit date:2018-02-27
Release date:2018-06-20
Last modified:2018-07-04
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural basis for the selective inhibition of activated thrombin-activatable fibrinolysis inhibitor (TAFIa) by a selenium-containing inhibitor with chloro-aminopyridine as a basic group
Bioorg. Med. Chem. Lett., 28, 2018
5XUQ
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH AN ANTAGONIST, 2-METHYLIDENE-19,26,27-TRINOR-22-(S)-BUTYL-1-HYDROXY-25-OXO-25-(1H-PYRROL-2-YL)- VITAMIN D3
Descriptor:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-one
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-24
Release date:2018-06-27
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Discovery of Potent Vitamin D Receptor Antagonist
To Be Published
5XPP
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 25RS-(HYDROXYPHENYL)-2-METHYLIDENE-19,26,27-TRINOR-1,25-DIHYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-03
Release date:2018-06-06
Last modified:2018-06-13
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
5XPO
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 25-(HYDROXYPHENYL)-2-METHYLIDENE-19,26,27-TRINOR-25-OXO-1-HYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-03
Release date:2018-06-06
Last modified:2018-06-13
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
5XPN
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 25RS-(HYDROXYPHENYL)-25-METHOXY-2-METHYLIDENE-19,26,27-TRINOR-1-HYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, ...
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-03
Release date:2018-07-11
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
5XPM
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 22S-BUTYL-25RS-(HYDROXYPHENYL)-25-METHOXY-2-METHYLIDENE-19,26,27-TRINOR-1-HYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, Mediator of RNA polymerase II transcription subunit 1, (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-03
Release date:2018-06-06
Last modified:2018-06-13
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
5XPL
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CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 22S-BUTYL-25-HYDROXYPHENYL-2-METHYLIDENE-19,26,27-TRINOR-25-OXO-1-HYDROXYVITAMIN D3
Descriptor:Vitamin D3 receptor, Nuclear receptor coactivator 2, (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one
Authors:Kato, A., Itoh, T., Yamamoto, K.
Deposit date:2017-06-03
Release date:2018-06-06
Last modified:2018-06-13
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60, 2017
5X7Y
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CRYSTAL STRUCTURE OF THE DOG LIPOCALIN ALLERGEN CAN F 6
Descriptor:Lipocalin-Can f 6 allergen, DI(HYDROXYETHYL)ETHER
Authors:Yamamoto, K., Otani, T., Sugiura, K., Nakatsuji, M., Nishimura, S., Inui, T.
Deposit date:2017-02-28
Release date:2018-04-04
Last modified:2019-03-06
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal structure of the dog allergen Can f 6 and structure-based implications of its cross-reactivity with the cat allergen Fel d 4.
Sci Rep, 9, 2019
5WZR
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ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM BIFIDUM - GAL-NHAC-DNJ COMPLEX
Descriptor:Alpha-N-acetylgalactosaminidase, ZINC ION, N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide, ...
Authors:Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.
Deposit date:2017-01-18
Release date:2017-06-07
Last modified:2017-08-02
Method:X-RAY DIFFRACTION (2.79 Å)
Cite:The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
5WZQ
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ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM BIFIDUM - QUADRUPLE MUTANT
Descriptor:Alpha-N-acetylgalactosaminidase, ZINC ION, GLYCEROL
Authors:Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.
Deposit date:2017-01-18
Release date:2017-06-07
Last modified:2017-08-02
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
5WZP
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ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM BIFIDUM - LIGAND FREE
Descriptor:Alpha-N-acetylgalactosaminidase, ZINC ION, CALCIUM ION
Authors:Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.
Deposit date:2017-01-18
Release date:2017-06-07
Last modified:2017-08-02
Method:X-RAY DIFFRACTION (2.64 Å)
Cite:The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
5WZN
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ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM BIFIDUM - GALNAC COMPLEX
Descriptor:Alpha-N-acetylgalactosaminidase, ZINC ION, N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE, ...
Authors:Sato, M., Arakawa, T., Ashida, H., Fushinobu, S.
Deposit date:2017-01-18
Release date:2017-06-07
Last modified:2017-08-02
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
5WR1
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COVALENT BOND FORMATION OF BIFUNCTIONAL LIGAND WITH HPPARG-LBD
Descriptor:Peroxisome proliferator-activated receptor gamma, 2-[E-(E-16-azido-2-oxidanylidene-hexadec-3-enylidene)amino]ethanoic acid
Authors:Kojima, H., Itoh, T., Yamamoto, K.
Deposit date:2016-11-29
Release date:2017-11-22
Last modified:2017-12-13
Method:X-RAY DIFFRACTION (2.34 Å)
Cite:On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
5WR0
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HUISGEN CYCLOADDITION FOR PPARG-LBD LABELING BY SOAKING METHOD
Descriptor:Peroxisome proliferator-activated receptor gamma, (E)-N-[(3E)-2-oxo-16-(8-{6-[(trifluoroacetyl)amino]hexanoyl}-8,9-dihydro-1H-dibenzo[b,f][1,2,3]triazolo[4,5-d]azocin-1-yl)hexadec-3-en-1-ylidene]glycine
Authors:Kojima, H., Itoh, T., Yamamoto, K.
Deposit date:2016-11-29
Release date:2017-11-22
Last modified:2017-12-13
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017
5WQX
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COVALENT BOND FORMATION OF SYNTHETIC LIGAND WITH HPPARG-LBD
Descriptor:Peroxisome proliferator-activated receptor gamma, 2-[E-(E-2-oxidanylidenehexadec-5-enylidene)amino]ethanoic acid
Authors:Kojima, H., Itoh, T., Yamamoto, K.
Deposit date:2016-11-29
Release date:2017-11-22
Last modified:2017-12-13
Method:X-RAY DIFFRACTION (2.29 Å)
Cite:On-site reaction for PPAR gamma modification using a specific bifunctional ligand
Bioorg. Med. Chem., 25, 2017