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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kikuzato, K."

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Search Summary

This query matches 13 Structures.

Refinements

Structure Determination Methodology

experimental (13)

Scientific Name of Source Organism

	Homo sapiens (9)
	Oryza sativa Japonica Group (3)
	Arabidopsis thaliana (1)

Taxonomy

Eukaryota (13)

Experimental Method

X-RAY DIFFRACTION (13)

Polymer Entity Type

Protein (13)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (8)
	2.0 - 2.5 (2)

Release Date

	2015 - 2019 (8)
	2020 - 2024 (5)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (3)

Symmetry Type

	Asymmetric (9)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a+b) (5)
	All beta proteins (5)
	Artifacts (5)

AllSelected

1 to 13 of 13 Structures

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5H09 \| pdb_00005h09	Download File View File

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

Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.

(2017) Bioorg Med Chem 25: 4259-4264

Released	2017-10-04
Method	X-RAY DIFFRACTION 1.945 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	OOO

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5H0B \| pdb_00005h0b	Download File View File

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

Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.

(2017) Bioorg Med Chem 25: 4259-4264

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.651 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	OOQ

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5H0E \| pdb_00005h0e	Download File View File

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

Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.

(2017) Bioorg Med Chem 25: 4259-4264

Released	2017-10-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	OOS

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5H0G \| pdb_00005h0g	Download File View File

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

Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.

(2017) Bioorg Med Chem 25: 4259-4264

Released	2017-10-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	OOU

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5H0H \| pdb_00005h0h	Download File View File

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

Tomabechi, Y., Kukimoto-Niino, M., Shirouzu, M.

(2017) Bioorg Med Chem 25: 4259-4264

Released	2017-10-04
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase HCK (protein)
Unique Ligands	OOV

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5ZHR \| pdb_00005zhr	Download File View File

Crystal structure of OsD14 in complex with covalently bound KK094

Hirabayashi, K., Miyakawa, T., Tanokura, M.

(2019) Mol Plant 12: 44-58

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	Strigolactone esterase D14 (protein)
Unique Ligands	KOK

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5ZHS \| pdb_00005zhs	Download File View File

Crystal structure of OsD14 in complex with covalently bound KK052

Hirabayashi, K., Miyakawa, T., Tanokura, M.

(2019) Mol Plant 12: 44-58

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.49 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	Strigolactone esterase D14 (protein)
Unique Ligands	KAT

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5ZHT \| pdb_00005zht	Download File View File

Crystal structure of OsD14 in complex with covalently bound KK073

Hirabayashi, K., Miyakawa, T., Tanokura, M.

(2019) Mol Plant 12: 44-58

Released	2018-11-21
Method	X-RAY DIFFRACTION 1.532 Å
Organisms	Oryza sativa Japonica Group
Macromolecule	Strigolactone esterase D14 (protein)
Unique Ligands	9GU

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7XUA \| pdb_00007xua	Download File View File

Structure of G9a in complex with compound 10a

Niwa, H., Shirai, F., Sato, S., Nishigaya, Y., Umehara, T.

(2023) J Med Chem 66: 4059-4085

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase EHMT2 (protein)
Unique Ligands	EDO, I5X, SFG, TRS, ZN

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7XUB \| pdb_00007xub	Download File View File

Structure of G9a in complex with compound 10d

Niwa, H., Shirai, F., Sato, S., Nishigaya, Y., Umehara, T.

(2023) J Med Chem 66: 4059-4085

Released	2023-03-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase EHMT2 (protein)
Unique Ligands	EDO, I6L, SFG, TRS, ZN

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7XUC \| pdb_00007xuc	Download File View File

Structure of G9a in complex with compound 11a

Niwa, H., Shirai, F., Sato, S., Nishigaya, Y., Umehara, T.

(2023) J Med Chem 66: 4059-4085

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase EHMT2 (protein)
Unique Ligands	CL, EDO, I6S, SFG, ZN

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7XUD \| pdb_00007xud	Download File View File

Structure of G9a in complex with compound 26a

Niwa, H., Shirai, F., Sato, S., Nishigaya, Y., Umehara, T.

(2023) J Med Chem 66: 4059-4085

Released	2023-03-29
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Histone-lysine N-methyltransferase EHMT2 (protein)
Unique Ligands	CL, EDO, I6Z, SFG, TRS, ZN

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8Y9O \| pdb_00008y9o	Download File View File

Crystal structure of AtKAI2 in complex with KK181N1

Wang, J.W., Miyakawa, T., Asami, T.

(2025) Nat Commun 16: 104-104

Released	2024-12-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Arabidopsis thaliana
Macromolecule	Probable esterase KAI2 (protein)
Unique Ligands	IB0

1 to 13 of 13 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

5H09 | pdb_00005h09

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

5H0B | pdb_00005h0b

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

5H0E | pdb_00005h0e

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

5H0G | pdb_00005h0g

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

5H0H | pdb_00005h0h

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

5ZHR | pdb_00005zhr

Crystal structure of OsD14 in complex with covalently bound KK094

5ZHS | pdb_00005zhs

Crystal structure of OsD14 in complex with covalently bound KK052

5ZHT | pdb_00005zht

Crystal structure of OsD14 in complex with covalently bound KK073

7XUA | pdb_00007xua

Structure of G9a in complex with compound 10a

7XUB | pdb_00007xub

Structure of G9a in complex with compound 10d

7XUC | pdb_00007xuc

Structure of G9a in complex with compound 11a

7XUD | pdb_00007xud

Structure of G9a in complex with compound 26a

8Y9O | pdb_00008y9o

Crystal structure of AtKAI2 in complex with KK181N1

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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

Symmetry Type

SCOP Classification

5H09 | pdb_00005h09

5H0B | pdb_00005h0b

5H0E | pdb_00005h0e

5H0G | pdb_00005h0g

5H0H | pdb_00005h0h

5ZHR | pdb_00005zhr

5ZHS | pdb_00005zhs

5ZHT | pdb_00005zht

7XUA | pdb_00007xua

7XUB | pdb_00007xub

7XUC | pdb_00007xuc

7XUD | pdb_00007xud

8Y9O | pdb_00008y9o