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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yu, D."

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Search Summary

This query matches 154 Structures.

Refinements

Structure Determination Methodology

experimental (154)

Scientific Name of Source Organism

	Homo sapiens (81)
	Clostridioides difficile (20)
	Clostridioides difficile 630 (9)
	synthetic construct (7)
	Arabidopsis thaliana (6)
	Saccharomyces cerevisiae (6)
	Escherichia coli K-12 (5)
	Saccharomyces cerevisiae S288C (5)
	Caenorhabditis elegans (4)
	Linum usitatissimum (4)

More...

Taxonomy

	Eukaryota (115)
	Bacteria (37)
	other sequences (7)
	Riboviria (6)
	Duplodnaviria (5)
	unclassified sequences (3)

Experimental Method

	X-RAY DIFFRACTION (110)
	ELECTRON MICROSCOPY (41)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (154)
	DNA (33)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (18)
	1.5 - 2.0 (34)
	2.0 - 2.5 (28)
	2.5 - 3.0 (32)
	3.0 - 3.5 (15)
	3.5 - 4.0 (11)
	4.0 - 4.5 (5)
	> 4.5 (8)

Release Date

	2005 - 2009 (10)
	2010 - 2014 (35)
	2015 - 2019 (25)
	2020 - 2024 (84)

Enzyme Classification Name

	Hydrolases (29)
	Transferases (83)
	Oxidoreductases (10)
	Ligases (18)

Membrane Protein Annotation

	PDBTM (2)
	MemProtMD (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (128)
	Cyclic (26)
	Dihedral (1)

SCOP Classification

	All alpha proteins (25)
	Alpha and beta proteins (a/b) (15)
	Alpha and beta proteins (a+b) (14)
	All beta proteins (4)
	Artifacts (2)

AllSelected

1 to 25 of 154 Structures

Page 1 of 7

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1WCI \| pdb_00001wci	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	CL, GOL, K, MN, WWF

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2BEU \| pdb_00002beu	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein) PEPTIDE ALA-TYR-ARG (protein)
Unique Ligands	CL, GOL, K, MN, SO4, THV

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2BEV \| pdb_00002bev	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein) PEPTIDE ALA-TYR-ARG (protein)
Unique Ligands	CL, GOL, K, MN, THY

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2BEW \| pdb_00002bew	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein) PEPTIDE ALA-TYR-ARG (protein)
Unique Ligands	CL, GOL, K, MN, THW

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2BFC \| pdb_00002bfc	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	GOL, K, MN, TZD

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2BFD \| pdb_00002bfd	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.39 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	CL, GOL, K, MN, MPD, TPP

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2BFE \| pdb_00002bfe	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	CL, GOL, K, MN, MRD, TPP

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2BFF \| pdb_00002bff	Download File View File

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

Released	2006-02-16
Method	X-RAY DIFFRACTION 1.46 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	GOL, K, MN, TZD

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2J9F \| pdb_00002j9f	Download File View File

Human branched-chain alpha-ketoacid dehydrogenase-decarboxylase E1b

Jun, L., Machius, M., Chuang, J.L., Wynn, R.M., Chuang, D.T.

(2007) J Biological Chem 282: 11904

Released	2007-02-27
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Homo sapiens
Macromolecule	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT (protein) 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT (protein)
Unique Ligands	GOL, K, MN, THV

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2X8D \| pdb_00002x8d	Download File View File

Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration

Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

(2010) Bioorg Med Chem 20: 5133

Released	2010-08-11
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	SO4, X8D

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2X8E \| pdb_00002x8e	Download File View File

Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration

Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

(2010) Bioorg Med Chem 20: 5133

Released	2010-08-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	SO4, X8E

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2X8I \| pdb_00002x8i	Download File View File

Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration

Read, J.A., Breed, J., Haye, H., McCall, E., Otterbein, L., Vallentine, A., White, A.

(2010) Bioorg Med Chem 20: 5133

Released	2010-08-11
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	GOL, SO4, X8I

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2YDI \| pdb_00002ydi	Download File View File

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas

Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

(2012) J Med Chem 55: 5130

Released	2012-04-04
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	SO4, YDI

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2YDJ \| pdb_00002ydj	Download File View File

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas

Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

(2012) J Med Chem 55: 5130

Released	2012-01-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	PO4, YDJ

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2YDK \| pdb_00002ydk	Download File View File

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas

Read, J.A., Breed, J., Haye, H., McCall, E., Rowsell, S., Vallentine, A., White, A.

(2012) J Med Chem 55: 5130

Released	2012-04-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	GOL, SO4, YDK

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2YER \| pdb_00002yer	Download File View File

Synthesis and evaluation of triazolones as checkpoint kinase 1 inhibitors

Read, J.A., Breed, J., Haye, H., McCall, E., Vallentine, A., White, A., Otterbein, L.

(2012) Bioorg Med Chem Lett 22: 2330

Released	2012-03-14
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	EDO, SO4, TQ1

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2YEX \| pdb_00002yex	Download File View File

Synthesis and evaluation of triazolones as checkpoint kinase 1 inhibitors

Read, J.A., Breed, J., Haye, H., McCall, E., Vallentine, A., White, A.

(2012) Bioorg Med Chem Lett 22: 2330

Released	2012-03-14
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE CHK1 (protein)
Unique Ligands	GOL, SO4, YEX

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3JZK \| pdb_00003jzk	Download File View File

crystal structure of MDM2 with chromenotriazolopyrimidine 1

Huang, X.

(2009) J Med Chem 52: 7044-7053

Released	2009-11-17
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	YIN

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3PZE \| pdb_00003pze	Download File View File

JNK1 in complex with inhibitor

Xue, Y.

(2012) J Med Chem 55: 5130-5142

Released	2011-12-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Mitogen-activated protein kinase 8 (protein)
Unique Ligands	CFK, SO4

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3U2Q \| pdb_00003u2q	Download File View File

EF-Tu (Escherichia coli) in complex with NVP-LFF571

Palestrant, D.J.

(2012) J Med Chem 55: 2376-2387

Released	2012-05-02
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli K-12 Planobispora rosea
Macromolecule	Elongation factor Tu 1 (protein) Thiocillin GE2270 analogue NVP-LFF571 (protein)
Unique Ligands	GDP, MG

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3U6B \| pdb_00003u6b	Download File View File

Ef-tu (escherichia coli) in complex with nvp-ldi028

Palestrant, D.J.

(2011) J Med Chem 54: 8099-8109

Released	2012-02-08
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Escherichia coli K-12 Planobispora rosea
Macromolecule	Elongation factor Tu 1 (protein) Thiocillin GE2270 analogue NVP-LDI028 (protein)
Unique Ligands	GDP, MG

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3U6K \| pdb_00003u6k	Download File View File

Ef-tu (escherichia coli) in complex with nvp-ldk733

Palestrant, D.J.

(2011) J Med Chem 54: 8099-8109

Released	2012-02-08
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Escherichia coli K-12 Planobispora rosea
Macromolecule	Elongation factor Tu 1 (protein) Thiocillin GE2270 analogue NVP-LDK733 (protein)
Unique Ligands	GDP, MG

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4AOJ \| pdb_00004aoj	Download File View File

Human TrkA in complex with the inhibitor AZ-23

Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., MacIntyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

(2012) ACS Med Chem Lett 3: 705

Released	2012-08-15
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Homo sapiens
Macromolecule	HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR (protein)
Unique Ligands	V4Z, ZN