3U19
 
 | | CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51 | | Descriptor: | GLYCEROL, artificial protein OR51 | | Authors: | Kuzin, A, Su, M, Seetharaman, J, Sahdev, S, Xiao, R, Kohan, E, Richter, F, Everett, J.K, Acton, T.B, Baker, D, Montelione, G.T, Hunt, J.F, Tong, L, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2011-09-29 | | Release date: | 2011-10-26 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE
ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51
To be Published
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4ONQ
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3NXF
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | Althoff, E.A, Jiang, L, Wang, L, Lassila, J.K, Moody, J, Bolduc, J, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D. | | Deposit date: | 2010-07-13 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
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2N2U
 | | Solution NMR Structure of DE NOVO DESIGNED Ferredoxin Fold PROTEIN sfr3, Northeast Structural Genomics Consortium (NESG) Target OR358 | | Descriptor: | OR358 | | Authors: | Liu, G, Lin, Y, Koga, N, Koga, R, Xiao, R, Janjua, H, Hamilton, K, Pederson, K, Acton, T.B, Kornhaber, G, Everett, J.K, Baker, D, Montelione, G.T, Northeast Structural Genomics Consortium (NESG) | | Deposit date: | 2015-05-14 | | Release date: | 2015-09-16 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Solution NMR Structure of DE NOVO DESIGNED Ferredoxin Fold PROTEIN sfr3, Northeast Structural Genomics Consortium (NESG) Target OR358
To be Published
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4ONJ
 | | Crystal structure of the catalytic domain of ntDRM | | Descriptor: | DNA methyltransferase, SINEFUNGIN | | Authors: | Du, J, Patel, D.J. | | Deposit date: | 2014-01-28 | | Release date: | 2014-06-04 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.807 Å) | | Cite: | Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Cell(Cambridge,Mass.), 157, 2014
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3O6Y
 | | Robust computational design, optimization, and structural characterization of retroaldol enzymes | | Descriptor: | Retro-Aldolase, SULFATE ION | | Authors: | Althoff, E.A, Wang, L, Jiang, L, Moody, J, Bolduc, J, Lassila, J.K, Wang, Z.Z, Smith, M, Hari, S, Herschlag, D, Stoddard, B.L, Baker, D. | | Deposit date: | 2010-07-29 | | Release date: | 2011-06-29 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.091 Å) | | Cite: | Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
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6Y7Y
 | | Fragments KCL_771 and KCL_802 in complex with MAP kinase p38-alpha | | Descriptor: | (2-azanyl-2-adamantyl)methanol, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, 6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridine-3-sulfonamide, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-02 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.51 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6Y80
 | | Fragment KCL_916 in complex with MAP kinase p38-alpha | | Descriptor: | 1-(2-adamantylmethyl)-3-ethyl-guanidine, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, CALCIUM ION, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-02 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.24 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6Y81
 | | Fragment KCL_1088 in complex with MAP kinase p38-alpha | | Descriptor: | (3~{R})-~{N}-[(2-azanyl-2-adamantyl)methyl]-3-[[6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridin-3-yl]sulfonylamino]-3-phenyl-propanamide, 1,2-ETHANEDIOL, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-03 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6YCW
 | | Fragment KCL_K767 in complex with MAP kinase p38-alpha | | Descriptor: | 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, CALCIUM ION, Mitogen-activated protein kinase 14, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-19 | | Release date: | 2020-04-08 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.34 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6Y7X
 | | Fragment KCL_771 in complex with MAP kinase p38-alpha | | Descriptor: | (2-azanyl-2-adamantyl)methanol, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, CALCIUM ION, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-02 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6YCU
 | | Fragment KCL_K777 in complex with MAP kinase p38-alpha | | Descriptor: | 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, 4-[2,5-bis(oxidanylidene)pyrrol-1-yl]-~{N}-propyl-benzenesulfonamide, CALCIUM ION, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-19 | | Release date: | 2020-04-08 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6Y7W
 | | Fragment KCL_1337 in complex with MAP kinase p38-alpha | | Descriptor: | (2~{R})-~{N}-[(2-azanyl-2-adamantyl)methyl]-4-[6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridin-3-yl]sulfonyl-2-methyl-morpholine-2-carboxamide, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, CALCIUM ION, ... | | Authors: | De Nicola, G.F, Nichols, C.E. | | Deposit date: | 2020-03-02 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.39 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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4HOP
 | | Crystal structure of the computationally designed NNOS-Syntrophin complex | | Descriptor: | Alpha-1-syntrophin, Nitric oxide synthase, brain | | Authors: | Harwood, I.M, Melero, C, Ollikainen, N, Kortemme, T. | | Deposit date: | 2012-10-22 | | Release date: | 2013-11-06 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.
Proc.Natl.Acad.Sci.USA, 111, 2014
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7BWN
 | | Crystal Structure of a Designed Protein Heterocatenane | | Descriptor: | Cellular tumor antigen p53, Chimera of Green fluorescent protein and p53dim | | Authors: | Liu, Y.J, Duan, Z.L, Fang, J, Zhang, F, Xiao, J.Y, Zhang, W.B. | | Deposit date: | 2020-04-15 | | Release date: | 2020-06-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.396 Å) | | Cite: | Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6SO2
 | | Fragment N13460a in complex with MAP kinase p38-alpha | | Descriptor: | CHLORIDE ION, MAGNESIUM ION, Mitogen-activated protein kinase 14, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-28 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SPL
 | | Fragment KCL615 in complex with MAP kinase p38-alpha | | Descriptor: | (5~{S},7~{R})-3-azanyladamantan-1-ol, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, CALCIUM ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-09-01 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SO1
 | | Fragment N13569a in complex with MAP kinase p38-alpha | | Descriptor: | 1-(1,3-benzodioxol-5-yl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine, CHLORIDE ION, MAGNESIUM ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-28 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.66 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SOI
 | | Fragment N13788a in complex with MAP kinase p38-alpha | | Descriptor: | CHLORIDE ION, DIMETHYL SULFOXIDE, MAGNESIUM ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-29 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SOT
 | | Fragment N11290a in complex with MAP kinase p38-alpha | | Descriptor: | 1,2-ETHANEDIOL, 1-(4-methylphenyl)pyrrolidine-2,5-dione, CHLORIDE ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-29 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SOD
 | | Fragment N14056a in complex with MAP kinase p38-alpha | | Descriptor: | 1-[[(3~{S})-1,4-dioxaspiro[4.5]decan-3-yl]methyl]piperidine, CHLORIDE ION, DIMETHYL SULFOXIDE, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-29 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.87 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SOU
 | | Fragment N13565a in complex with MAP kinase p38-alpha | | Descriptor: | 2-(4-methylphenoxy)-1-(4-methylpiperazin-4-ium-1-yl)ethanone, CHLORIDE ION, Mitogen-activated protein kinase 14, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-29 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SO4
 | | Fragment RZ132 in complex with MAP kinase p38-alpha | | Descriptor: | (2~{S})-2-methyl-4-(oxetan-3-yl)-~{N}-(phenylmethyl)piperazine-2-carboxamide, CHLORIDE ION, MAGNESIUM ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-29 | | Release date: | 2019-09-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.51 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SP9
 | | Fragment KCL802 in complex with MAP kinase p38-alpha | | Descriptor: | 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, 6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridine-3-sulfonamide, CALCIUM ION, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-31 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.22 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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6SOV
 | | Fragments KCL_615 and KCL_802 in complex with MAP kinase p38-alpha | | Descriptor: | (5~{S},7~{R})-3-azanyladamantan-1-ol, 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE, 6-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]pyridine-3-sulfonamide, ... | | Authors: | Nichols, C.E, De Nicola, G.F. | | Deposit date: | 2019-08-30 | | Release date: | 2019-10-02 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.31 Å) | | Cite: | Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
J.Med.Chem., 63, 2020
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