RCSB PDB: Search

5V7I \| pdb_00005v7i	Download File View File

Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile

Ducker, G.S., Ghergurovich, J.M., Mainolfi, N., Suri, V., Jeong, S., Friedman, A., Manfredi, M., Kim, H., Rabinowitz, J.D.

(2017) Proc Natl Acad Sci U S A 114: 11404-11409

Released	2017-10-11
Method	X-RAY DIFFRACTION 2.47 Å
Organisms	Homo sapiens
Macromolecule	Serine hydroxymethyltransferase, mitochondrial (protein)
Unique Ligands	8Z1, GLY, GOL, PEG

Explore in 3D

6QMR \| pdb_00006qmr	Download File View File

Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid

Karki, R., Powers, J., Mainolfi, N., Anderson, K., Belanger, D., Liu, D., Jendza, K., Gelin, C.F., Solovay, C., Mac Sweeeny, A., Delgado, O., Crowley, M., Liao, S.-M., Argikar, U.A., Flohr, S., La Bonte, L.R., Lorthiois, E.L., Vulpetti, A., Cumin, F., Brown, A., Adams, C., Jaffee, B., Mogi, M.

(2019) J Med Chem 62: 4656-4668

Released	2019-04-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Complement factor D (protein)
Unique Ligands	J6T

Explore in 3D

6QMT \| pdb_00006qmt	Download File View File

Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid

Karki, R., Powers, J., Mainolfi, N., Anderson, K., Belanger, D., Liu, D., Jendza, K., Gelin, C.F., Solovay, C., Mac Sweeeny, A., Delgado, O., Crowley, M., Liao, S.-M., Argikar, U.A., Flohr, S., La Bonte, L.R., Lorthiois, E.L., Vulpetti, A., Cumin, F., Brown, A., Adams, C., Jaffee, B., Mogi, M.

(2019) J Med Chem 62: 4656-4668

Released	2019-04-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Complement factor D (protein)
Unique Ligands	J7B

Explore in 3D

6QSW \| pdb_00006qsw	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.

Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGT, SO4

Explore in 3D

6QSX \| pdb_00006qsx	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.

Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGN, SO4, ZN

Explore in 3D

6RAV \| pdb_00006rav	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid

Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-04-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGQ, SO4, ZN

Explore in 3D

6T8U \| pdb_00006t8u	Download File View File

Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine

Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Mac Sweeney, A., Wiesmann, C., Adams, C., Liao, S.-M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Serrano-Wu, M., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., De Erkenez, A., Yang, L., Fang, L., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

(2020) J Med Chem 63: 5697-5722

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.84 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	MVZ, SO4

Explore in 3D

6T8V \| pdb_00006t8v	Download File View File

Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole

Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Mac Sweeney, A., Wiesmann, C., Adams, C., Mainolfi, N., Liao, S.-M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Serrano-Wu, M., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., De Erkenez, A., Yang, L., Fang, L., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Wiesmann, C., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

(2020) J Med Chem 63: 5697-5722

Released	2020-03-04
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	MVK, SO4, ZN

Explore in 3D

6T8W \| pdb_00006t8w	Download File View File

Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid

Mainolfi, N., Ehara, T., Karki, R.G., Anderson, K., Sweeney, A.M., Wiesmann, C., Adams, C., Mainolfi, N., Liao, S.M., Argikar, U.A., Jendza, K., Zhang, C., Powers, J., Klosowski, D.W., Crowley, M., Kawanami, T., Ding, J., April, M., Forster, C., Wu, M.S., Capparelli, M., Ramqaj, R., Solovay, C., Cumin, F., Smith, T.M., Ferrara, L., Lee, W., Long, D., Prentiss, M., Erkenez, A.D., Yang, L., Fang, L., Sellner, H., Sirockin, F., Valeur, E., Erbel, P., Ramage, P., Gerhartz, B., Schubart, A., Flohr, S., Gradoux, N., Feifel, R., Vogg, B., Wiesmann, C., Maibaum, J., Eder, J., Sedrani, R., Harrison, R.A., Mogi, M., Jaffee, B.D., Adams, C.M.

(2020) J Med Chem 63: 5697-5722

Released	2020-03-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	MVW, SO4, ZN

Explore in 3D

8V1O \| pdb_00008v1o	Download File View File

Crystal structure of IRAK4 kinase domain with compound 4

Weiss, M.M., Zheng, X., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Sharma, K., Shi, Y., Slavin, A., Walter, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Ji, N., Walker, D., Mainolfi, N.

(2024) J Med Chem 67: 10548-10566

Released	2024-07-03
Method	X-RAY DIFFRACTION 2.92 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-1 receptor-associated kinase 4 (protein)
Unique Ligands	CL, GOL, SO4, Y9T

Explore in 3D

8V2F \| pdb_00008v2f	Download File View File

Crystal structure of IRAK4 kinase domain with compound 9

Weiss, M.M., Zheng, X., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Sharma, K., Shi, Y., Slavin, A., Walter, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Ji, N., Walker, D., Mainolfi, N.

(2024) J Med Chem 67: 10548-10566

Released	2024-07-03
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-1 receptor-associated kinase 4 (protein)
Unique Ligands	CL, GOL, YJU

Explore in 3D

8V2L \| pdb_00008v2l	Download File View File

Crystal structure of IRAK4 kinase domain with compound 8

Weiss, M.M., Zheng, X., Browne, C.M., Campbell, V., Chen, D., Enerson, B., Fei, X., Huang, X., Klaus, C.R., Li, H., Mayo, M., McDonald, A.A., Paul, A., Sharma, K., Shi, Y., Slavin, A., Walter, D.M., Yuan, K., Zhang, Y., Zhu, X., Kelleher, J., Ji, N., Walker, D., Mainolfi, N.

(2024) J Med Chem 67: 10548-10566

Released	2024-07-03
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens
Macromolecule	Interleukin-1 receptor-associated kinase 4 (protein)
Unique Ligands	EDO, YK0

Explore in 3D

9CUO \| pdb_00009cuo	Download File View File

Crystal structure of CRBN with compound 3

Zheng, X., Ji, N., Campbell, V., Slavin, A., Zhu, X., Chen, D., Rong, H., Enerson, B., Mayo, M., Sharma, K., Browne, C.M., Klaus, C.R., Li, H., Massa, G., McDonald, A.A., Shi, Y., Sintchak, M., Skouras, S., Walther, D.M., Yuan, K., Zhang, Y., Kelleher, J., Guang, L., Luo, X., Mainolfi, N., Weiss, M.M.

(2024) J Med Chem 67: 18022-18037

Released	2024-08-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Protein cereblon (protein)
Unique Ligands	A1A0J, EDO, SO4, ZN

5V7I | pdb_00005v7i

Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile

6QMR | pdb_00006qmr

Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid

6QMT | pdb_00006qmt

Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid

6QSW | pdb_00006qsw

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.

6QSX | pdb_00006qsx

Complement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.

6RAV | pdb_00006rav

Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid

6T8U | pdb_00006t8u

Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine

6T8V | pdb_00006t8v

Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole

6T8W | pdb_00006t8w

Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid

8V1O | pdb_00008v1o

Crystal structure of IRAK4 kinase domain with compound 4

8V2F | pdb_00008v2f

Crystal structure of IRAK4 kinase domain with compound 9

8V2L | pdb_00008v2l

Crystal structure of IRAK4 kinase domain with compound 8

9CUO | pdb_00009cuo

Crystal structure of CRBN with compound 3

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

5V7I | pdb_00005v7i

6QMR | pdb_00006qmr

6QMT | pdb_00006qmt

6QSW | pdb_00006qsw

6QSX | pdb_00006qsx

6RAV | pdb_00006rav

6T8U | pdb_00006t8u

6T8V | pdb_00006t8v

6T8W | pdb_00006t8w

8V1O | pdb_00008v1o

8V2F | pdb_00008v2f

8V2L | pdb_00008v2l

9CUO | pdb_00009cuo