RCSB PDB: Search

3QCQ \| pdb_00003qcq	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-(3-Amino-1H-indazol-6-yl)-N4-ethyl-2,4-pyrimidinediamine

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.501 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q0, GOL, SO4

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3QCS \| pdb_00003qcs	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-[2-Amino-6-(4-morpholinyl)-4-pyrimidinyl]-1H-indazol-3-amine

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.487 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q1, GOL, SO4

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3QCX \| pdb_00003qcx	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-{2-Amino-6-[(3R)-3-methyl-4-morpholinyl]-4-pyrimidinyl}-1H-indazol-3-amine

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q2, GOL, SO4

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3QCY \| pdb_00003qcy	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 4-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-N-phenyl-2-morpholinecarboxamide

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q3, GOL, SO4

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3QD0 \| pdb_00003qd0	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with (2R,5S)-1-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-N-phenyl-3-piperidinecarboxamide

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q4, GOL, SO4

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3QD3 \| pdb_00003qd3	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl {(3R,6S)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}carbamate

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q5, GOL, SO4

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3QD4 \| pdb_00003qd4	Download File View File

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl{(3R,5R)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-5-methyl-3-piperidinyl}carbamate

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

Released	2011-03-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide-dependent protein kinase 1 (protein)
Unique Ligands	3Q6, SO4

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4G31 \| pdb_00004g31	Download File View File

Crystal Structure of GSK6414 Bound to PERK (R587-R1092, delete A660-T867) at 2.28 A Resolution

Gampe, R.T., Axten, J.M.

(2012) J Med Chem 55: 7193-7207

Released	2012-08-08
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 2-alpha kinase 3 (protein)
Unique Ligands	0WH, GOL

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4G34 \| pdb_00004g34	Download File View File

Crystal Structure of GSK6924 Bound to PERK (R587-R1092, delete A660-T867) at 2.70 A Resolution

Gampe, R.T., Axten, J.M.

(2012) J Med Chem 55: 7193-7207

Released	2012-08-08
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 2-alpha kinase 3 (protein)
Unique Ligands	924

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4M7I \| pdb_00004m7i	Download File View File

Crystal Structure of GSK6157 Bound to PERK (R587-R1092, delete A660-T867) at 2.34A Resolution

Gampe, R.T., Axten, J.M.

To be published

Released	2014-09-03
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Homo sapiens
Macromolecule	Eukaryotic translation initiation factor 2-alpha kinase 3 (protein)
Unique Ligands	27D

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6X9I \| pdb_00006x9i	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, GOL, SAH, ZN

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6X9J \| pdb_00006x9j	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, X52, ZN

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6X9K \| pdb_00006x9k	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, UXM, ZN

3QCQ | pdb_00003qcq

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-(3-Amino-1H-indazol-6-yl)-N4-ethyl-2,4-pyrimidinediamine

3QCS | pdb_00003qcs

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-[2-Amino-6-(4-morpholinyl)-4-pyrimidinyl]-1H-indazol-3-amine

3QCX | pdb_00003qcx

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 6-{2-Amino-6-[(3R)-3-methyl-4-morpholinyl]-4-pyrimidinyl}-1H-indazol-3-amine

3QCY | pdb_00003qcy

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 4-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-N-phenyl-2-morpholinecarboxamide

3QD0 | pdb_00003qd0

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with (2R,5S)-1-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-N-phenyl-3-piperidinecarboxamide

3QD3 | pdb_00003qd3

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl {(3R,6S)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}carbamate

3QD4 | pdb_00003qd4

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl{(3R,5R)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-5-methyl-3-piperidinyl}carbamate

4G31 | pdb_00004g31

Crystal Structure of GSK6414 Bound to PERK (R587-R1092, delete A660-T867) at 2.28 A Resolution

4G34 | pdb_00004g34

Crystal Structure of GSK6924 Bound to PERK (R587-R1092, delete A660-T867) at 2.70 A Resolution

4M7I | pdb_00004m7i

Crystal Structure of GSK6157 Bound to PERK (R587-R1092, delete A660-T867) at 2.34A Resolution

6X9I | pdb_00006x9i

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA

6X9J | pdb_00006x9j

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

6X9K | pdb_00006x9k

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

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Structure Determination Methodology

Scientific Name of Source Organism

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Experimental Method

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Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3QCQ | pdb_00003qcq

3QCS | pdb_00003qcs

3QCX | pdb_00003qcx

3QCY | pdb_00003qcy

3QD0 | pdb_00003qd0

3QD3 | pdb_00003qd3

3QD4 | pdb_00003qd4

4G31 | pdb_00004g31

4G34 | pdb_00004g34

4M7I | pdb_00004m7i

6X9I | pdb_00006x9i

6X9J | pdb_00006x9j

6X9K | pdb_00006x9k