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232,059 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Nakabayashi, M."

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Search Summary

This query matches 44 Structures.

Refinements

Structure Determination Methodology

experimental (44)

Scientific Name of Source Organism

	Rattus norvegicus (27)
	Homo sapiens (8)
	Xenopus tropicalis (6)
	Aeropyrum pernix K1 (4)
	Linum usitatissimum (3)
	Parafontaria falcifera (2)
	Pyrococcus furiosus (2)
	Thermus thermophilus HB8 (2)
	Niallia circulans (1)
	Parafontaria laminata (1)

More...

Taxonomy

	Eukaryota (34)
	Archaea (7)
	Eukaryota (eukaryotes) (6)
	Bacteria (3)

Experimental Method

X-RAY DIFFRACTION (44)

Polymer Entity Type

Protein (44)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (15)
	2.0 - 2.5 (20)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (9)
	2010 - 2014 (19)
	2015 - 2019 (4)
	2020 - 2024 (11)
	2025 - 2029 (1)

Enzyme Classification Name

	Lyases (7)
	Transferases (4)
	Hydrolases (3)
	Oxidoreductases (1)

Symmetry Type

	Asymmetric (35)
	Cyclic (7)
	Dihedral (3)

SCOP Classification

	Alpha and beta proteins (a/b) (6)
	All alpha proteins (8)
	Alpha and beta proteins (a+b) (1)
	Artifacts (1)

AllSelected

1 to 25 of 44 Structures

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2D4R	Download File View File

Crystal structure of TTHA0849 from Thermus thermophilus HB8

Nakabayashi, M., Shibata, N., Kuramitsu, S., Higuchi, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 1027-1031

Released	2005-12-13
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus HB8
Macromolecule	hypothetical protein TTHA0849 (protein)
Unique Ligands	SO4

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2ZL9	Download File View File

2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure

Shimizu, M., Miyamoto, Y., Nakabayashi, M., Masuno, H., Ikura, T., Ito, N.

(2008) Bioorg Med Chem 16: 6949-6964

Released	2008-06-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Rattus norvegicus
Macromolecule	Coactivator peptide DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	VDA

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2ZLA	Download File View File

2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure

Shimizu, M., Miyamoto, Y., Nakabayashi, M., Masuno, H., Ikura, T., Ito, N.

(2008) Bioorg Med Chem 16: 6949-6964

Released	2008-06-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus
Macromolecule	Coactivator peptide DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	VDB

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2ZLC	Download File View File

2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure

Shimizu, M., Miyamoto, Y., Nakabayashi, M., Masuno, H., Ikura, T., Ito, N.

(2008) Bioorg Med Chem 16: 6949-6964

Released	2008-06-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus
Macromolecule	Coactivator peptide DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	VDX

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2ZMH	Download File View File

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

Nakabayashi, M., Yamada, S., Tanaka, T., Igarashi, M., Yoshimoto, N., Ikura, T., Ito, N., Makishima, M., Tokiwa, H., DeLuca, H.F., Shimizu, M.

(2008) J Med Chem 51: 5320-5329

Released	2008-09-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	NYA

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2ZMI	Download File View File

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

Nakabayashi, M., Yamada, S., Tanaka, T., Igarashi, M., Yoshimoto, N., Ikura, T., Ito, N., Makishima, M., Tokiwa, H., DeLuca, H.F., Shimizu, M.

(2008) J Med Chem 51: 5320-5329

Released	2008-09-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	EDO, FMT, TT2

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2ZMJ	Download File View File

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

Nakabayashi, M., Yamada, S., Tanaka, T., Igarashi, M., Yoshimoto, N., Ikura, T., Ito, N., Makishima, M., Tokiwa, H., DeLuca, H.F., Shimizu, M.

(2008) J Med Chem 51: 5320-5329

Released	2008-09-02
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	MI4

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2ZXM	Download File View File

A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

Nakabayashi, M., Ikura, T., Ito, N.

(2009) J Med Chem 52: 1438-1449

Released	2009-02-17
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	JB1

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2ZXN	Download File View File

A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

Nakabayashi, M., Ikura, T., Ito, N.

(2009) J Med Chem 52: 1438-1449

Released	2009-02-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	JC1

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3AFR	Download File View File

Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex

Inaba, Y., Nakabayashi, M., Itoh, T., Ikura, T., Ito, N., Yamamoto, K.

(2010) J Steroid Biochem Mol Biol 121: 146-150

Released	2010-03-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus Xenopus tropicalis
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	ICJ

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3VJS	Download File View File

Vitamin D receptor complex with a carborane compound

Fujii, S., Masuno, M., Kagechika, H., Nakabayashi, M., Ito, N.

(2011) J Am Chem Soc 133: 20933-20941

Released	2012-02-08
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Vitamin D3 receptor (protein) peptide from Mediator of RNA polymerase II transcription subunit 1 (protein)
Unique Ligands	10S

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3VJT	Download File View File

Vitamin D receptor complex with a carborane compound

Fujii, S., Masuno, M., Kagechika, H., Nakabayashi, M., Ito, N.

(2011) J Am Chem Soc 133: 20933-20941

Released	2012-02-08
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	Vitamin D3 receptor (protein) peptide from Mediator of RNA polymerase II transcription subunit 1 (protein)
Unique Ligands	10R

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3VRT	Download File View File

VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3

Nakabayashi, M., Yoshimoto, N., Inaba, Y., Itoh, T., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS2

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3VRU	Download File View File

VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS3

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3VRV	Download File View File

VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YSD

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3VRW	Download File View File

VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3

Yoshimoto, N., Inaba, Y., Itoh, T., Nakabayashi, M., Ito, N., Yamamoto, K.

(2012) J Med Chem 55: 4373-4381

Released	2012-05-23
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Rattus norvegicus
Macromolecule	13-meric peptide from Mediator of RNA polymerase II transcription subunit 1 (protein) Vitamin D3 receptor (protein)
Unique Ligands	YS5

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3VT3	Download File View File

Crystal structures of rat VDR-LBD with R270L mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	EDO, FMT, VDX

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3VT4	Download File View File

Crystal structures of rat VDR-LBD with R270L mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	5YI

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3VT5	Download File View File

Crystal structures of rat VDR-LBD with R270L mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 2.11 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	YI2

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3VT6	Download File View File

Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	5YI

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3VT7	Download File View File

Crystal structures of rat VDR-LBD with W282R mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	VDX

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3VT8	Download File View File

Crystal structures of rat VDR-LBD with W282R mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	YI3

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3VT9	Download File View File

Crystal structures of rat VDR-LBD with W282R mutation

Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

(2013) J Med Chem 56: 6745-6760

Released	2013-05-22
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	YI4

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3VTB	Download File View File

Crystal structure of rat vitamin D receptor bound to a partial agonist 25-adamantyl-23-yne-19-norvitammin D ADTK1

Nakabayashi, M., Kudo, T., Tokiwa, H., Makishima, M., Yamada, S., Ikura, T., Ito, N.

(2014) J Med Chem

Released	2013-06-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	TKA

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3VTC	Download File View File

Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3

Nakabayashi, M., Kudo, T., Tokiwa, H., Makishima, M., Yamada, S., Ikura, T., Ito, N.

(2014) J Med Chem

Released	2013-06-12
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Rattus norvegicus
Macromolecule	COACTIVATOR PEPTIDE DRIP (protein) Vitamin D3 receptor (protein)
Unique Ligands	EDO, TK3

1 to 25 of 44 Structures

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