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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nakabayashi, M."

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Search Summary

This query matches 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

	Rattus norvegicus (28)
	Homo sapiens (9)
	Xenopus tropicalis (6)
	Aeropyrum pernix K1 (4)
	Thermostichus vulcanus (4)
	Linum usitatissimum (3)
	Parafontaria falcifera (2)
	Pyrococcus furiosus (2)
	Thermus thermophilus HB8 (2)
	Niallia circulans (1)

More...

Taxonomy

	Eukaryota (35)
	Archaea (7)
	Bacteria (7)
	Eukaryota (eukaryotes) (6)

Experimental Method

X-RAY DIFFRACTION (49)

Polymer Entity Type

Protein (49)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (4)
	1.5 - 2.0 (15)
	2.0 - 2.5 (22)
	2.5 - 3.0 (6)
	3.0 - 3.5 (1)

Release Date

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

Enzyme Classification Name

	Oxidoreductases (5)
	Transferases (4)
	Lyases (7)
	Hydrolases (3)

Membrane Protein Annotation

	MemProtMD (4)
	PDBTM (4)
	mpstruc (4)

Symmetry Type

	Asymmetric (40)
	Cyclic (7)
	Dihedral (3)

SCOP Classification

	Membrane and cell surface proteins and peptides (4)
	Alpha and beta proteins (a/b) (6)
	All alpha proteins (12)
	Artifacts (4)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 49 Structures

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2D4R \| pdb_00002d4r	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 \| pdb_00002zl9	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 \| pdb_00002zla	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 \| pdb_00002zlc	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 \| pdb_00002zmh	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 \| pdb_00002zmi	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 \| pdb_00002zmj	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 \| pdb_00002zxm	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 \| pdb_00002zxn	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 \| pdb_00003afr	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 \| pdb_00003vjs	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 \| pdb_00003vjt	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 \| pdb_00003vrt	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 \| pdb_00003vru	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 \| pdb_00003vrv	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 \| pdb_00003vrw	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 \| pdb_00003vt3	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 \| pdb_00003vt4	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 \| pdb_00003vt5	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 \| pdb_00003vt6	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 \| pdb_00003vt7	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 \| pdb_00003vt8	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 \| pdb_00003vt9	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 \| pdb_00003vtb	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 \| pdb_00003vtc	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 49 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2D4R | pdb_00002d4r

2ZL9 | pdb_00002zl9

2ZLA | pdb_00002zla

2ZLC | pdb_00002zlc

2ZMH | pdb_00002zmh

2ZMI | pdb_00002zmi

2ZMJ | pdb_00002zmj

2ZXM | pdb_00002zxm

2ZXN | pdb_00002zxn

3AFR | pdb_00003afr

3VJS | pdb_00003vjs

3VJT | pdb_00003vjt

3VRT | pdb_00003vrt

3VRU | pdb_00003vru

3VRV | pdb_00003vrv

3VRW | pdb_00003vrw

3VT3 | pdb_00003vt3

3VT4 | pdb_00003vt4

3VT5 | pdb_00003vt5

3VT6 | pdb_00003vt6

3VT7 | pdb_00003vt7

3VT8 | pdb_00003vt8

3VT9 | pdb_00003vt9

3VTB | pdb_00003vtb

3VTC | pdb_00003vtc