RCSB PDB: Search

4OYS \| pdb_00004oys	Download File View File

CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.

Mathieu, M., Marquette, J.p.

(2014) Nat Chem Biol 10: 1013-1019

Released	2014-10-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	1TT, SO4

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4PH4 \| pdb_00004ph4	Download File View File

The crystal structure of Human VPS34 in complex with PIK-III

Knapp, M.S., Elling, R.A.

(2014) Nat Cell Biol 16: 1069-1079

Released	2014-10-29
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	2UG, GOL

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5DFZ \| pdb_00005dfz	Download File View File

Structure of Vps34 complex II from S. cerevisiae.

Rostislavleva, K., Soler, N., Ohashi, Y., Zhang, L., Williams, R.L.

(2015) Science 350: aac7365-aac7365

Released	2015-10-07
Method	X-RAY DIFFRACTION 4.4 Å
Organisms	Lama glama Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 6

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5ENN \| pdb_00005enn	Download File View File

The crystal structure of Human VPS34 in complex with a selective and potent inhibitor

Kearney, E.P.

To be published

Released	2016-11-16
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	5QS, GOL, NA, SO4

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5KC2 \| pdb_00005kc2	Download File View File

Negative stain structure of Vps15/Vps34 complex

Kirsten, M.L., Zhang, L., Ohashi, Y., Perisic, O., Williams, R.L., Sachse, C.

(2016) Autophagy 12: 2129-2144

Released	2016-10-05
Method	ELECTRON MICROSCOPY 28 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Phosphatidylinositol 3-kinase VPS34 (protein) Serine/threonine-protein kinase VPS15 (protein)

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6HOG \| pdb_00006hog	Download File View File

Structure of VPS34 LIR motif bound to GABARAP

Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S., Lamark, T., Johansen, T.

(2019) Autophagy 15: 1333-1355

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.26 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein (protein)
Unique Ligands	EDO, GOL, SO4

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6HOH \| pdb_00006hoh	Download File View File

Structure of VPS34 LIR motif (S249E) bound to GABARAP

Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S., Lamark, T., Johansen, T.

(2019) Autophagy 15: 1333-1355

Released	2019-02-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein (protein)
Unique Ligands	PGE

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6I3U \| pdb_00006i3u	Download File View File

Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept study in Huntington's disease models

Leonard, P.M.

(2019) J Med Chem 62: 2988-3008

Released	2019-03-20
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	H2E

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6YKG \| pdb_00006ykg	Download File View File

Structure-based exploration of selectivity for ATM inhibitors in Huntingtons disease

Van de Poel, A., Leonard, P.M., Lamers, M.B.A.C.

(2021) J Med Chem 64: 5018-5036

Released	2021-04-14
Method	X-RAY DIFFRACTION 3.12 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	OZ8

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7BL1 \| pdb_00007bl1	Download File View File

human complex II-BATS bound to membrane-attached Rab5a-GTP

Tremel, S., Morado, D.R., Kovtun, O., Williams, R.L., Briggs, J.A.G., Munro, S., Ohashi, Y., Bertram, J., Perisic, O.

(2021) Nat Commun 12: 1564-1564

Released	2021-03-03
Method	ELECTRON MICROSCOPY 9.8 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6
Unique Ligands	GTP, MG

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7RSJ \| pdb_00007rsj	Download File View File

Structure of the VPS34 kinase domain with compound 14

Hu, D.X., Patel, S., Chen, H., Wang, S., Staben, S., Dimitrova, Y.N., Wallweber, H.A., Lee, J.Y., Chan, G.K.Y., Sneeringer, C.J., Prangley, M.S., Moffat, J.G., Wu, C., Schutt, L.K., Salphati, L., Pang, J., McNamara, E., Huang, H., Chen, Y., Wang, Y., Zhao, W., Lim, J., Murthy, A., Siu, M.

(2022) J Med Chem 65: 11500-11512

Released	2021-11-24
Method	X-RAY DIFFRACTION 1.881 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	7IH, EDO, GOL, NA

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7RSP \| pdb_00007rsp	Download File View File

Structure of the VPS34 kinase domain with compound 14

Hu, D.X., Patel, S., Chen, H., Wang, S., Staben, S., Dimitrova, Y.N., Wallweber, H.A., Lee, J.Y., Chan, G.K.Y., Sneeringer, C.J., Prangley, M.S., Moffat, J.G., Wu, C., Schutt, L.K., Salphati, L., Pang, J., McNamara, E., Huang, H., Chen, Y., Wang, Y., Zhao, W., Lim, J., Murthy, A., Siu, M.

(2022) J Med Chem 65: 11500-11512

Released	2021-11-24
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	7IK, GOL

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7RSV \| pdb_00007rsv	Download File View File

Structure of the VPS34 kinase domain with compound 5

Hu, D.X., Patel, S., Chen, H., Wang, S., Staben, S., Dimitrova, Y.N., Wallweber, H.A., Lee, J.Y., Chan, G.K.Y., Sneeringer, C.J., Prangley, M.S., Moffat, J.G., Wu, C., Schutt, L.K., Salphati, L., Pang, J., McNamara, E., Huang, H., Chen, Y., Wang, Y., Zhao, W., Lim, J., Murthy, A., Siu, M.

(2022) J Med Chem 65: 11500-11512

Released	2021-11-24
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	7IQ, GOL, NA

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8RXR \| pdb_00008rxr	Download File View File

Crystal structure of VPS34 in complex with inhibitor SB02024

Tresaugues, L., Yu, Y., Bogdan, M., Parpal, S., Silvander, C., Lindstrom, J., Simeon, J., Timson, M.J., Al-Hashimi, H., Smith, B.D., Flynn, D.L., Viklund, J., Martinsson, J., De Milito, A., Andersson, M.

(2024) Mol Oncol 18: 1904-1922

Released	2024-03-20
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	A1H4E, DMS, GOL, IMD, PEG

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8SOR \| pdb_00008sor	Download File View File

Structure of human PI3KC3-C1 complex

Chen, M., Hurley, J.H.

(2023) bioRxiv

Released	2023-06-21
Method	ELECTRON MICROSCOPY 3.96 Å
Organisms	Homo sapiens
Macromolecule	Beclin 1-associated autophagy-related key regulator (protein) Beclin-1 (protein) Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein) Phosphoinositide 3-kinase regulatory subunit 4 (protein)
Unique Ligands	ADP

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9C82 \| pdb_00009c82	Download File View File

Structure of human ULK1C:PI3KC3-C1 supercomplex

Chen, M., Hurley, J.H.

(2023) bioRxiv

Released	2024-07-03
Method	ELECTRON MICROSCOPY 6.84 Å
Organisms	Homo sapiens
Macromolecule	Beclin 1-associated autophagy-related key regulator (protein) Beclin-1 (protein) Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein) Phosphoinositide 3-kinase regulatory subunit 4 (protein) RB1-inducible coiled-coil protein 1 (protein)

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9E4V \| pdb_00009e4v	Download File View File

The structure of human vacuolar protein sorting 34 catalytic domain bound to MES

Abiodun, W.O., Fullmer, A., Tsubaki, E., Doukov, T., Moody, J.D.

To be published

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein)
Unique Ligands	CL, DMS, GOL, K, MES, PEG, PG4

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9MHF \| pdb_00009mhf	Download File View File

Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)

Cook, A.S.I., Hurley, J.H., Chen, M.

To be published

Released	2025-02-12
Method	ELECTRON MICROSCOPY 2.73 Å
Organisms	Homo sapiens
Macromolecule	Beclin 1-associated autophagy-related key regulator (protein) Beclin-1 (protein) Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein) Phosphoinositide 3-kinase regulatory subunit 4 (protein) Ras-related protein Rab-1A (protein)
Unique Ligands	GTP, MG, MYR

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9MHG \| pdb_00009mhg	Download File View File

Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation

Cook, A.S.I., Hurley, J.H., Chen, M.

To be published

Released	2025-02-12
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens
Macromolecule	Beclin 1-associated autophagy-related key regulator (protein) Beclin-1 (protein) Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein) Phosphoinositide 3-kinase regulatory subunit 4 (protein) Ras-related protein Rab-1A (protein)
Unique Ligands	GTP, MG, MYR

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9MHH \| pdb_00009mhh	Download File View File

PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation

Cook, A.S.I., Hurley, J.H., Chen, M.

To be published

Released	2025-02-12
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Homo sapiens
Macromolecule	Beclin 1-associated autophagy-related key regulator (protein) Beclin-1 (protein) Phosphatidylinositol 3-kinase catalytic subunit type 3 (protein) Phosphoinositide 3-kinase regulatory subunit 4 (protein) Ras-related protein Rab-1A (protein)
Unique Ligands	GTP, MG

4OYS | pdb_00004oys

CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.

4PH4 | pdb_00004ph4

The crystal structure of Human VPS34 in complex with PIK-III

5DFZ | pdb_00005dfz

Structure of Vps34 complex II from S. cerevisiae.

5ENN | pdb_00005enn

The crystal structure of Human VPS34 in complex with a selective and potent inhibitor

5KC2 | pdb_00005kc2

Negative stain structure of Vps15/Vps34 complex

6HOG | pdb_00006hog

Structure of VPS34 LIR motif bound to GABARAP

6HOH | pdb_00006hoh

Structure of VPS34 LIR motif (S249E) bound to GABARAP

6I3U | pdb_00006i3u

Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept study in Huntington's disease models

6YKG | pdb_00006ykg

Structure-based exploration of selectivity for ATM inhibitors in Huntingtons disease

7BL1 | pdb_00007bl1

human complex II-BATS bound to membrane-attached Rab5a-GTP

7RSJ | pdb_00007rsj

Structure of the VPS34 kinase domain with compound 14

7RSP | pdb_00007rsp

Structure of the VPS34 kinase domain with compound 14

7RSV | pdb_00007rsv

Structure of the VPS34 kinase domain with compound 5

8RXR | pdb_00008rxr

Crystal structure of VPS34 in complex with inhibitor SB02024

8SOR | pdb_00008sor

Structure of human PI3KC3-C1 complex

9C82 | pdb_00009c82

Structure of human ULK1C:PI3KC3-C1 supercomplex

9E4V | pdb_00009e4v

The structure of human vacuolar protein sorting 34 catalytic domain bound to MES

9MHF | pdb_00009mhf

Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)

9MHG | pdb_00009mhg

Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation

9MHH | pdb_00009mhh

PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation

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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

4OYS | pdb_00004oys

4PH4 | pdb_00004ph4

5DFZ | pdb_00005dfz

5ENN | pdb_00005enn

5KC2 | pdb_00005kc2

6HOG | pdb_00006hog

6HOH | pdb_00006hoh

6I3U | pdb_00006i3u

6YKG | pdb_00006ykg

7BL1 | pdb_00007bl1

7RSJ | pdb_00007rsj

7RSP | pdb_00007rsp

7RSV | pdb_00007rsv

8RXR | pdb_00008rxr

8SOR | pdb_00008sor

9C82 | pdb_00009c82

9E4V | pdb_00009e4v

9MHF | pdb_00009mhf

9MHG | pdb_00009mhg

9MHH | pdb_00009mhh