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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "DPDE3"

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Search Summary

This query matches 96 Structures.

Refinements

Structure Determination Methodology

experimental (96)

Scientific Name of Source Organism

Homo sapiens (96)

Taxonomy

Eukaryota (96)

Experimental Method

X-RAY DIFFRACTION (96)

Polymer Entity Type

Protein (96)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (39)
	2.0 - 2.5 (45)
	2.5 - 3.0 (6)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (13)
	2015 - 2019 (42)
	2020 - 2024 (32)
	2025 - 2029 (6)

Enzyme Classification Name

Hydrolases (96)

Symmetry Type

	Asymmetric (50)
	Cyclic (45)
	Dihedral (2)

SCOP Classification

	All alpha proteins (59)
	Artifacts (12)

AllSelected

1 to 25 of 96 Structures

Page 1 of 4

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2QYN \| pdb_00002qyn	Download File View File

Crystal structure of PDE4D2 in complex with inhibitor NPV

Ke, H.

(2007) Biochem J 408: 193-201

Released	2008-04-08
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	MG, NPV, ZN

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3G4G \| pdb_00003g4g	Download File View File

Crystal structure of human phosphodiesterase 4d with regulatory domain and d155871

Staker, B.L.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	CA, D71, MG, ZN

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3G4I \| pdb_00003g4i	Download File View File

Crystal structure of human phosphodiesterase 4d with d155871

Staker, B.L.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-19
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	D71, EOH, MG, SO4, ZN

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3G4K \| pdb_00003g4k	Download File View File

Crystal structure of human phosphodiesterase 4d with rolipram

Staker, B.L.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-19
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	EDO, MG, ROL, SO4, ZN

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3G4L \| pdb_00003g4l	Download File View File

Crystal structure of human phosphodiesterase 4d with roflumilast

Staker, B.L.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	EDO, MG, ROF, SO4, ZN

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3G58 \| pdb_00003g58	Download File View File

Crystal structure of human phosphodiesterase 4d with d155988/pmnpq

Staker, B.L.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	988, EDO, MG, SO4, ZN

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3IAD \| pdb_00003iad	Download File View File

Crystal structure of human phosphodiesterase 4D with bound allosteric modulator

Staker, B.L., Burgin Jr., A.B.

(2010) Nat Biotechnol 28: 63-70

Released	2010-01-05
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	15X, EPE, MG, ZN

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3IAK \| pdb_00003iak	Download File View File

Crystal structure of human phosphodiesterase 4d (PDE4d) with papaverine.

Cheng, R.K.Y., Crawley, L., Barker, J., Wood, M., Felicetti, B., Whittaker, M.

To be published

Released	2009-09-08
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	EV1, MG, ZN

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3K4S \| pdb_00003k4s	Download File View File

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

To be published

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	0MO, MG, ZN

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3SL3 \| pdb_00003sl3	Download File View File

Crystal structure of the apo form of the catalytic domain of PDE4D2

Feil, S.F.

(2011) Bioorg Med Chem Lett 21: 7089-7093

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	DMS, EDO, EPE, PEG, PO4, ZN

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3SL4 \| pdb_00003sl4	Download File View File

Crystal structure of the catalytic domain of PDE4D2 with compound 10D

Feil, S.F.

(2011) Bioorg Med Chem Lett 21: 7089-7093

Released	2011-10-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	DMS, EDO, EPE, JN4, PEG, PO4, ZN

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3SL5 \| pdb_00003sl5	Download File View File

Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d

Feil, S.F.

(2011) Bioorg Med Chem Lett 21: 7089-7093

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	DMS, EDO, EPE, J25, ZN

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3SL6 \| pdb_00003sl6	Download File View File

Crystal structure of the catalytic domain of PDE4D2 with compound 12c

Feil, S.F.

(2011) Bioorg Med Chem Lett 21: 7089-7093

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	DMS, EDO, EPE, JN8, ZN

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3SL8 \| pdb_00003sl8	Download File View File

Crystal structure of the catalytic domain of PDE4D2 with compound 10o

Feil, S.F.

(2011) Bioorg Med Chem Lett 21: 7089-7093

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	DMS, EDO, JN7, PEG, PO4, ZN

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4OGB \| pdb_00004ogb	Download File View File

Crystal structure of the catalytic domain of PDE4D2 with compound 2

Feil, S.C., Parker, M.W.

To be published

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.032 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	2SR, DMS, EDO, EPE, PEG, ZN

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4W1O \| pdb_00004w1o	Download File View File

PDE4D complexed with inhibitor

Sorensen, M.D.

(2014) J Med Chem 57: 5893-5903

Released	2014-11-05
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	3GJ, ZN

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4WCU \| pdb_00004wcu	Download File View File

PDE4 complexed with inhibitor

Sorensen, M.D.

(2014) J Med Chem 57: 5893-5903

Released	2014-10-08
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	3KQ, MG, ZN

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5K1I \| pdb_00005k1i	Download File View File

PDE4 crystal structure in complex with small molecule inhibitor

Segarra, V., Hernandez, B., Ferrer-Miralles, N., Korndoerfer, I., Aymami, J.

(2016) J Med Chem 59: 10479-10497

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	6PT, MG, ZN

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5K32 \| pdb_00005k32	Download File View File

PDE4D crystal structure in complex with small molecule inhibitor

Segarra, V., Hernandez, B., Roberts, R., Gracia, J., Soler, M., Bonin, I., Aymami, J.

(2018) J Med Chem 61: 2472-2489

Released	2017-03-29
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	6Q2, EDO, MG, ZN

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5LBO \| pdb_00005lbo	Download File View File

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001

Singh, A.K., Brown, D.G.

(2018) J Med Chem 61: 3870-3888

Released	2018-03-14
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	6M5, DTT, EDO, EPE, MG, PEG, ZN

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5TKB \| pdb_00005tkb	Download File View File

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH A TETRAFLUORANLINE COMPOUND

Sack, J.S.

(2017) Medchemcomm 8: 700-712

Released	2016-12-28
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	7DJ, EOH, MG, SO4, ZN

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5WH5 \| pdb_00005wh5	Download File View File

Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91

Wang, H.

(2018) Biochemistry 57: 4518-4525

Released	2018-07-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	MG, R91, ZN

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5WH6 \| pdb_00005wh6	Download File View File

Crystal structure of PDE4D2 in complex with inhibitor (S_Zl-n-91)

Ke, H., Wang, H.

(2018) Biochemistry 57: 4518-4525

Released	2018-07-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	AKJ, MG, ZN

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5WQA \| pdb_00005wqa	Download File View File

Crystal structure of PDE4D catalytic domain complexed with Selaginpulvilins K

Huang, Y., Zhang, T., Zheng, X., Yin, S., Luo, H.B.

(2017) Biochem Pharmacol 130: 51-59

Released	2017-02-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	J20, MG, ZN

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6BOJ \| pdb_00006boj	Download File View File

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

Fox III, D., Fairman, J.W., Gurney, M.E.

(2018) Neuropsychopharmacology 43: 2299-2309

Released	2018-08-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (protein)
Unique Ligands	CL, E31, MG, MPD, ZN

1 to 25 of 96 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

Symmetry Type

SCOP Classification

2QYN | pdb_00002qyn

3G4G | pdb_00003g4g

3G4I | pdb_00003g4i

3G4K | pdb_00003g4k

3G4L | pdb_00003g4l

3G58 | pdb_00003g58

3IAD | pdb_00003iad

3IAK | pdb_00003iak

3K4S | pdb_00003k4s

3SL3 | pdb_00003sl3

3SL4 | pdb_00003sl4

3SL5 | pdb_00003sl5

3SL6 | pdb_00003sl6

3SL8 | pdb_00003sl8

4OGB | pdb_00004ogb

4W1O | pdb_00004w1o

4WCU | pdb_00004wcu

5K1I | pdb_00005k1i

5K32 | pdb_00005k32

5LBO | pdb_00005lbo

5TKB | pdb_00005tkb

5WH5 | pdb_00005wh5

5WH6 | pdb_00005wh6

5WQA | pdb_00005wqa

6BOJ | pdb_00006boj