3INM
 
 | | Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+) | | Descriptor: | 2-OXOGLUTARIC ACID, CALCIUM ION, GLYCEROL, ... | | Authors: | Fontano, E, Brown, R.S, Suto, R.K, Bhyravbhatla, B. | | Deposit date: | 2009-08-12 | | Release date: | 2009-11-24 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Cancer-associated IDH1 mutations produce 2-hydroxyglutarate.
Nature, 462, 2009
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6YWC
 | | De novo designed protein 4E1H_95 in complex with 101F antibody | | Descriptor: | Antibody 101F, Heavy Chain, light chain, ... | | Authors: | Yang, C, Sesterhenn, F, Pojer, F, Correia, B.E. | | Deposit date: | 2020-04-29 | | Release date: | 2020-10-07 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Bottom-up de novo design of functional proteins with complex structural features.
Nat.Chem.Biol., 17, 2021
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6YWD
 | | De novo designed protein 4H_01 in complex with Mota antibody | | Descriptor: | Antibody Mota, Heavy Chain, Light Chain, ... | | Authors: | Yang, C, Sesterhenn, F, Pojer, F, Correia, B.E. | | Deposit date: | 2020-04-29 | | Release date: | 2020-10-07 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Bottom-up de novo design of functional proteins with complex structural features.
Nat.Chem.Biol., 17, 2021
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2QXZ
 | | pectate lyase R236F from Xanthomonas campestris | | Descriptor: | PHOSPHATE ION, pectate lyase II | | Authors: | Garron, M.L, Shaya, D. | | Deposit date: | 2007-08-13 | | Release date: | 2008-03-04 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.12 Å) | | Cite: | Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment.
Appl.Environ.Microbiol., 74, 2008
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8OYS
 | | De novo designed TIM barrel fold TBF_24 | | Descriptor: | CHLORIDE ION, De novo designed TIM-barrel | | Authors: | Pacesa, M, Correia, B.E. | | Deposit date: | 2023-05-05 | | Release date: | 2023-10-18 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (1.34 Å) | | Cite: | Computational design of soluble and functional membrane protein analogues.
Nature, 631, 2024
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8OYV
 | | De novo designed Claudin fold CLF_4 | | Descriptor: | De novo designed soluble Claudin | | Authors: | Pacesa, M, Correia, B.E. | | Deposit date: | 2023-05-05 | | Release date: | 2023-10-18 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (2.79 Å) | | Cite: | Computational design of soluble and functional membrane protein analogues.
Nature, 631, 2024
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8OYX
 | | De novo designed soluble GPCR-like fold GLF_18 | | Descriptor: | De novo designed soluble GPCR-like protein, PHOSPHATE ION | | Authors: | Pacesa, M, Correia, B.E. | | Deposit date: | 2023-05-05 | | Release date: | 2023-10-18 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Computational design of soluble and functional membrane protein analogues.
Nature, 631, 2024
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8OYW
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8OYY
 | | De novo designed soluble GPCR-like fold GLF_32 | | Descriptor: | CHLORIDE ION, De novo designed soluble GPCR-like protein, POTASSIUM ION | | Authors: | Pacesa, M, Correia, B.E. | | Deposit date: | 2023-05-05 | | Release date: | 2023-10-18 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Computational design of soluble and functional membrane protein analogues.
Nature, 631, 2024
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6VTW
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9BEI
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6S3D
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6TPR
 | | PqsR (MvfR) bound to inhibitory compound 40 | | Descriptor: | 2-[(5-methyl-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]-~{N}-(4-pyridin-2-yloxyphenyl)ethanamide, Transcriptional regulator MvfR | | Authors: | Richardson, W.K, Emsley, J. | | Deposit date: | 2019-12-14 | | Release date: | 2020-05-13 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Hit Identification of New Potent PqsR Antagonists as Inhibitors of Quorum Sensing in Planktonic and Biofilm GrownPseudomonas aeruginosa.
Front Chem, 8, 2020
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7M4T
 | | Menin bound to M-1121 | | Descriptor: | Menin, methyl {(1S,2R)-2-[(1S)-2-(azetidin-1-yl)-1-(3-fluorophenyl)-1-{1-[(3-methoxy-1-{4-[(1S,4S)-5-propanoyl-2,5-diazabicyclo[2.2.1]heptane-2-sulfonyl]phenyl}azetidin-3-yl)methyl]piperidin-4-yl}ethyl]cyclopentyl}carbamate, praseodymium triacetate | | Authors: | Stuckey, J. | | Deposit date: | 2021-03-22 | | Release date: | 2021-08-11 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.74 Å) | | Cite: | Discovery of M-1121 as an Orally Active Covalent Inhibitor of Menin-MLL Interaction Capable of Achieving Complete and Long-Lasting Tumor Regression.
J.Med.Chem., 64, 2021
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8BD9
 | | Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10 | | Descriptor: | 1,3-dimethylbenzimidazol-2-one, CALCIUM ION, E3 ubiquitin-protein ligase TRIM33, ... | | Authors: | Tassone, G, Pozzi, C, Palomba, T. | | Deposit date: | 2022-10-18 | | Release date: | 2022-12-07 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design.
Int J Mol Sci, 23, 2022
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8BDY
 | | Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 9 | | Descriptor: | 1,3-dimethylbenzimidazol-2-one, CALCIUM ION, E3 ubiquitin-protein ligase TRIM33, ... | | Authors: | Tassone, G, Pozzi, C, Palomba, T. | | Deposit date: | 2022-10-20 | | Release date: | 2022-12-07 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design.
Int J Mol Sci, 23, 2022
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8BD8
 | | Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 8 | | Descriptor: | 1,3-dimethylbenzimidazol-2-one, CALCIUM ION, E3 ubiquitin-protein ligase TRIM33, ... | | Authors: | Tassone, G, Pozzi, C, Palomba, T. | | Deposit date: | 2022-10-18 | | Release date: | 2022-12-07 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design.
Int J Mol Sci, 23, 2022
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7ZSD
 | | cryo-EM structure of omicron spike in complex with de novo designed binder, local | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, de novo designed binder | | Authors: | Pablo, G, Sarah, W, Alexandra, V.H, Anthony, M, Andreas, S, Zander, H, Dongchun, N, Shuguang, T, Freyr, S, Casper, G, Priscilla, T, Alexandra, T, Stephane, R, Sandrine, G, Jane, M, Aaron, P, Zepeng, X, Yan, C, Pu, H, George, G, Elisa, O, Beat, F, Didier, T, Henning, S, Michael, B, Bruno, E.C. | | Deposit date: | 2022-05-06 | | Release date: | 2023-03-01 | | Last modified: | 2023-05-24 | | Method: | ELECTRON MICROSCOPY (3.29 Å) | | Cite: | De novo design of protein interactions with learned surface fingerprints.
Nature, 617, 2023
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7ZSS
 | | cryo-EM structure of D614 spike in complex with de novo designed binder | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ... | | Authors: | Pablo, G, Sarah, W, Alexandra, V.H, Anthony, M, Andreas, S, Zander, H, Dongchun, N, Shuguang, T, Freyr, S, Casper, G, Priscilla, T, Alexandra, T, Stephane, R, Sandrine, G, Jane, M, Aaron, P, Zepeng, X, Yan, C, Pu, H, George, G, Elisa, O, Beat, F, Didier, T, Henning, S, Michael, B, Bruno, E.C. | | Deposit date: | 2022-05-08 | | Release date: | 2023-03-01 | | Last modified: | 2023-05-24 | | Method: | ELECTRON MICROSCOPY (2.63 Å) | | Cite: | De novo design of protein interactions with learned surface fingerprints.
Nature, 617, 2023
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7ZRV
 | | cryo-EM structure of omicron spike in complex with de novo designed binder, full map | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein,Envelope glycoprotein, ... | | Authors: | Pablo, G, Sarah, W, Alexandra, V.H, Anthony, M, Andreas, S, Zander, H, Dongchun, N, Shuguang, T, Freyr, S, Casper, G, Priscilla, T, Alexandra, T, Stephane, R, Sandrine, G, Jane, M, Aaron, P, Zepeng, X, Yan, C, Pu, H, George, G, Elisa, O, Beat, F, Didier, T, Henning, S, Michael, B, Bruno, E.C. | | Deposit date: | 2022-05-05 | | Release date: | 2023-03-08 | | Last modified: | 2023-05-24 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | De novo design of protein interactions with learned surface fingerprints.
Nature, 617, 2023
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7XYQ
 | | Crystal strucutre of PD-L1 and the computationally designed DBL1_03 protein binder | | Descriptor: | ARGININE, CD274 molecule, DBL1_03 | | Authors: | Liu, K, Xu, Z, Han, P, Pacesa, M, Gao, G.F, Chai, Y, Tan, S. | | Deposit date: | 2022-06-02 | | Release date: | 2023-04-12 | | Last modified: | 2023-05-17 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | De novo design of protein interactions with learned surface fingerprints.
Nature, 617, 2023
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6TGD
 | | Crystal structure of NDM-1 in complex with triazole-based inhibitor OP31 | | Descriptor: | 4-[[(2~{S})-oxolan-2-yl]methyl]-3-pyridin-3-yl-1~{H}-1,2,4-triazole-5-thione, CALCIUM ION, Metallo-beta-lactamase NDM-1, ... | | Authors: | Maso, L, Spirakis, F, Santucci, M, Simon, C, Docquier, J.D, Cruciani, G, Costi, M.P, Tondi, D, Cendron, L. | | Deposit date: | 2019-11-15 | | Release date: | 2020-08-26 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases.
Sci Rep, 10, 2020
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6TGI
 | | Crystal structure of VIM-2 in complex with triazole-based inhibitor OP24 | | Descriptor: | 5-(4-chloranyl-1,5-dimethyl-pyrazol-3-yl)-4-ethyl-1,2,4-triazole-3-thiol, FORMIC ACID, Vim-1, ... | | Authors: | Maso, L, Spirakis, F, Santucci, M, Simon, C, Docquier, J.D, Cruciani, G, Costi, M.P, Tondi, D, Cendron, L. | | Deposit date: | 2019-11-15 | | Release date: | 2020-10-14 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Virtual screening identifies broad-spectrum beta-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases.
Sci Rep, 10, 2020
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7RWH
 | | Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-41998 | | Descriptor: | 1,2-ETHANEDIOL, 8-(4-bromophenyl)-6-(4-methoxyphenyl)-2-[2,2,2-tris(fluoranyl)ethylamino]pyrido[4,3-d]pyrimidin-7-ol, CHLORIDE ION, ... | | Authors: | Jin, L, Padyana, A.K. | | Deposit date: | 2021-08-19 | | Release date: | 2022-03-23 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.17 Å) | | Cite: | Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads.
J.Med.Chem., 65, 2022
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7RWG
 | | "Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor AGI-43192 | | Descriptor: | (8R)-8-(4-chlorophenyl)-6-(2-methyl-2H-indazol-5-yl)-2-[(2,2,2-trifluoroethyl)amino]-5,8-dihydropyrido[4,3-d]pyrimidin-7(6H)-one, 1,2-ETHANEDIOL, CHLORIDE ION, ... | | Authors: | Jin, L, Padyana, A.K. | | Deposit date: | 2021-08-19 | | Release date: | 2022-03-23 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (0.97 Å) | | Cite: | Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads.
J.Med.Chem., 65, 2022
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