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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Berger, R."

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Search Summary

This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Homo sapiens (9)
	Human alphaherpesvirus 1 (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (9)
	Duplodnaviria (1)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (10)

Polymer Entity Type

	Protein (10)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (7)
	3.5 - 4.0 (1)

Release Date

	2015 - 2019 (9)
	2020 - 2024 (1)

Enzyme Classification Name

	Hydrolases (9)
	Transferases (1)

Symmetry Type

	Asymmetric (7)
	Cyclic (3)

SCOP Classification

	All beta proteins (3)
	Small proteins (3)

AllSelected

1 to 10 of 10 Structures

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Explore in 3D

4YZU \| pdb_00004yzu	Download File View File

Rapid development of two Factor IXa inhibitors from Hit to Lead

Hruza, A., Reichert, P.

(2015) Bioorg Med Chem Lett 25: 2321-2325

Released	2015-05-20
Method	X-RAY DIFFRACTION 1.41 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein)
Unique Ligands	4K6, CL, NA, NHE

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4Z0K \| pdb_00004z0k	Download File View File

Rapid development of two Factor IXa inhibitors from Hit to Lead

Hruza, A., Reichert, P.

(2015) Bioorg Med Chem Lett 25: 2321-2325

Released	2015-05-20
Method	X-RAY DIFFRACTION 1.41 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein)
Unique Ligands	4LN, CL, NA, NHE

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5EGM \| pdb_00005egm	Download File View File

Development of a novel tricyclic class of potent and selective FIXa inhibitors

Meng, D., Andre, P., Bateman, T.J., Berger, R., Chen, Y., Desai, K., Dewnani, S., Ellsworth, K., Feng, D., Geissler, W.M., Guo, L., Hruza, A., Jian, T., Li, H., Parker, D.L., Reichert, P., Sherer, E.C., Smith, C.J., Sonatore, L.M., Tschirret-Guth, R., Wu, J., Xu, J., Zhang, T., Campeau, L., Orr, R., Poirier, M., McCabe-Dunn, j., Araki, K., Nishimura, T., Sakurada, I., Hirabayashi, T., Wood, H.B.

(2015) Bioorg Med Chem Lett 25: 5437-5443

Released	2015-11-18
Method	X-RAY DIFFRACTION 1.841 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein)
Unique Ligands	5NY, NA, NHE

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6B96 \| pdb_00006b96	Download File View File

Crystal Structure of PDE2 in complex with compound 16

Lu, J.

(2017) Bioorg Med Chem Lett 27: 5167-5171

Released	2017-11-22
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	CZV, EDO, MG, ZN

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6B97 \| pdb_00006b97	Download File View File

Crystal structure of PDE2 in complex with complex 9

Lu, J.

(2017) Bioorg Med Chem Lett 27: 5167-5171

Released	2017-11-22
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	CZY, EDO, MG, ZN

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6B98 \| pdb_00006b98	Download File View File

PDE2 in complex with compound 1

Lu, J.

(2017) Bioorg Med Chem Lett 27: 5167-5171

Released	2017-11-22
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	D07, MG, ZN

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6CYB \| pdb_00006cyb	Download File View File

PDE2 in complex with compound 7

Lu, J.

(2018) ACS Med Chem Lett 9: 815-820

Released	2018-09-19
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	EDO, FKV, MG, ZN

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6CYC \| pdb_00006cyc	Download File View File

PDE2 in complex with compound 5

Lu, J.

(2018) ACS Med Chem Lett 9: 815-820

Released	2018-09-19
Method	X-RAY DIFFRACTION 1.54 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	EDO, FKJ, MG, ZN

Explore in 3D

6CYD \| pdb_00006cyd	Download File View File

PDE2 in complex with compound 7

Lu, J.

(2018) ACS Med Chem Lett 9: 815-820

Released	2018-09-19
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Homo sapiens
Macromolecule	cGMP-dependent 3',5'-cyclic phosphodiesterase (protein)
Unique Ligands	EDO, FKG, MG, ZN

Explore in 3D

8VQ2 \| pdb_00008vq2	Download File View File

HSV1 polymerase ternary complex with dsDNA and compound 44

Hayes, R.P., Heo, M.R., Plotkin, M.

(2024) ACS Med Chem Lett 15: 1232-1241

Released	2024-08-28
Method	X-RAY DIFFRACTION 3.829 Å
Organisms	Human alphaherpesvirus 1 synthetic construct
Macromolecule	DNA polymerase (protein) DNA (5'-D(PAPTPCPCPTPTPCPCPCPCPTPAPC)-3') (nucleic acid) DNA (5'-D(PTPGPGPTPAPGPGPGPGPAPAPGPGPAPT)-3') (nucleic acid)
Unique Ligands	A1AC6

1 to 10 of 10 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.

4YZU | pdb_00004yzu

Rapid development of two Factor IXa inhibitors from Hit to Lead

4Z0K | pdb_00004z0k

Rapid development of two Factor IXa inhibitors from Hit to Lead

5EGM | pdb_00005egm

Development of a novel tricyclic class of potent and selective FIXa inhibitors

6B96 | pdb_00006b96

Crystal Structure of PDE2 in complex with compound 16

6B97 | pdb_00006b97

Crystal structure of PDE2 in complex with complex 9

6B98 | pdb_00006b98

PDE2 in complex with compound 1

6CYB | pdb_00006cyb

PDE2 in complex with compound 7

6CYC | pdb_00006cyc

PDE2 in complex with compound 5

6CYD | pdb_00006cyd

PDE2 in complex with compound 7

8VQ2 | pdb_00008vq2

HSV1 polymerase ternary complex with dsDNA and compound 44

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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

4YZU | pdb_00004yzu

4Z0K | pdb_00004z0k

5EGM | pdb_00005egm

6B96 | pdb_00006b96

6B97 | pdb_00006b97

6B98 | pdb_00006b98

6CYB | pdb_00006cyb

6CYC | pdb_00006cyc

6CYD | pdb_00006cyd

8VQ2 | pdb_00008vq2