2P83
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![BU of 2p83 by Molmil](/molmil-images/mine/2p83) | Potent and selective isophthalamide S2 hydroxyethylamine inhibitor of BACE1 | Descriptor: | Beta-secretase 1, N~3~-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-N~1~,N~1~-DIPROPYLBENZENE-1,3,5-TRICARBOXAMIDE, PHOSPHATE ION | Authors: | Benson, T.E, Prince, D.B, Tomasselli, A.G, Emmons, T.L, Paddock, D.J. | Deposit date: | 2007-03-21 | Release date: | 2007-06-19 | Last modified: | 2017-10-18 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Potent and selective isophthalamide S(2) hydroxyethylamine inhibitors of BACE1. Bioorg.Med.Chem.Lett., 17, 2007
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2WJO
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2P4J
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![BU of 2p4j by Molmil](/molmil-images/mine/2p4j) | Crystal structure of beta-secretase bond to an inhibitor with Isophthalamide Derivatives at P2-P3 | Descriptor: | Beta-secretase 1, N-[(1S,2S,4R)-2-HYDROXY-1-ISOBUTYL-5-({(1S)-1-[(ISOPROPYLAMINO)CARBONYL]-2-METHYLPROPYL}AMINO)-4-METHYL-5-OXOPENTYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE | Authors: | Hong, L, Ghosh, A.K, Tang, J. | Deposit date: | 2007-03-12 | Release date: | 2007-07-24 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Design, synthesis, and X-ray structure of potent memapsin 2 (beta-secretase) inhibitors with isophthalamide derivatives as the P2-P3-ligands. J.Med.Chem., 50, 2007
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3BUG
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![BU of 3bug by Molmil](/molmil-images/mine/3bug) | BACE-1 complexed with compound 3 | Descriptor: | 4-(2-aminoethyl)-2-ethylphenol, BETA-SECRETASE 1 | Authors: | Kuglstatter, A, Hennig, M. | Deposit date: | 2008-01-02 | Release date: | 2008-03-11 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Tyramine fragment binding to BACE-1 Bioorg.Med.Chem.Lett., 18, 2008
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3TPL
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![BU of 3tpl by Molmil](/molmil-images/mine/3tpl) | APO Structure of BACE1 | Descriptor: | Beta-secretase 1, CHLORIDE ION, SULFATE ION | Authors: | Xu, Y.C, Li, M.J, Greenblatt, H, Chen, T.T, Silman, I, Sussman, J.L. | Deposit date: | 2011-09-08 | Release date: | 2011-11-23 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations Acta Crystallogr.,Sect.D, 68, 2012
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2FDP
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![BU of 2fdp by Molmil](/molmil-images/mine/2fdp) | Crystal structure of beta-secretase complexed with an amino-ethylene inhibitor | Descriptor: | Beta-secretase 1, N1-((2S,3S,5R)-3-AMINO-6-(4-FLUOROPHENYLAMINO)-5-METHYL-6-OXO-1-PHENYLHEXAN-2-YL)-N3,N3-DIPROPYLISOPHTHALAMIDE | Authors: | Yang, W, Lu, W, Lu, Y, Zhong, M, Sun, J, Thomas, A.E, Wilkinson, J.M, Fucini, R.V, Lam, M, Randal, M, Shi, X.P, Jacobs, J.W, McDowell, R.S, Gordon, E.M, Ballinger, M.D. | Deposit date: | 2005-12-14 | Release date: | 2006-01-24 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1. J.Med.Chem., 49, 2006
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3WB5
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![BU of 3wb5 by Molmil](/molmil-images/mine/3wb5) | Crystal Structure of beta secetase in complex with (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-3,4,5,6-tetrahydropyrimidin-4-one | Descriptor: | (6S)-2-amino-3,6-dimethyl-6-[(1R,2R)-2-phenylcyclopropyl]-5,6-dihydropyrimidin-4(3H)-one, Beta-secretase 1, DIMETHYL SULFOXIDE, ... | Authors: | Yonezawa, S, Fujiwara, K, Yamamoto, T, Hattori, K, Yamakawa, H, Muto, C, Hosono, M, Tanaka, Y, Nakano, T, Takemoto, H, Arisawa, M, Shuto, S. | Deposit date: | 2013-05-13 | Release date: | 2013-10-02 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.501 Å) | Cite: | Conformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations Bioorg.Med.Chem., 21, 2013
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3UDK
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![BU of 3udk by Molmil](/molmil-images/mine/3udk) | Crystal Structure of BACE with Compound 6 | Descriptor: | 1,2-ETHANEDIOL, Beta-secretase 1, DI(HYDROXYETHYL)ETHER, ... | Authors: | Efremov, I.V, Vajdos, F.F, Borzilleri, K, Capetta, S, Dorff, P, Dutra, J, Mansour, M, Oborski, C, O'Connell, T, O'Sullivan, T.J, Pandit, J, Wang, H, Withka, J. | Deposit date: | 2011-10-28 | Release date: | 2012-04-18 | Last modified: | 2018-04-04 | Method: | X-RAY DIFFRACTION (2.51 Å) | Cite: | Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design. J.Med.Chem., 55, 2012
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5TOL
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![BU of 5tol by Molmil](/molmil-images/mine/5tol) | CRYSTAL STRUCTURE OF BETA-SITE APP-CLEAVING ENZYME 1 COMPLEXED WITH N-(3-((4AS,7AS)-2-AMINO-4,4A,5,6-TETRAHYDRO-7AH-FURO[2,3-D][1,3]THIAZIN-7A-YL)-4-FLUOROPHENYL)-5-BROMO-2-PYRIDINECARBOXAMIDE | Descriptor: | Beta-secretase 1, N-{3-[(4aR,7aR)-2-amino-4,4a,5,6-tetrahydro-7aH-furo[2,3-d][1,3]thiazin-7a-yl]-4-fluorophenyl}-5-bromopyridine-2-carboxamide | Authors: | Muckelbauer, J.K. | Deposit date: | 2016-10-18 | Release date: | 2016-11-23 | Last modified: | 2016-12-07 | Method: | X-RAY DIFFRACTION (2.51 Å) | Cite: | Discovery of furo[2,3-d][1,3]thiazinamines as beta amyloid cleaving enzyme-1 (BACE1) inhibitors. Bioorg.Med.Chem.Lett., 26, 2016
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5QD6
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![BU of 5qd6 by Molmil](/molmil-images/mine/5qd6) | Crystal structure of BACE complex with BMC004 | Descriptor: | (3S,14R,16S)-16-[1,1-dihydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione, Beta-secretase 1 | Authors: | Rondeau, J.M, Shao, C, Yang, H, Burley, S.K. | Deposit date: | 2017-12-01 | Release date: | 2020-06-03 | Last modified: | 2021-02-10 | Method: | X-RAY DIFFRACTION (2.51 Å) | Cite: | D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J.Comput.Aided Mol.Des., 34, 2020
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5MXD
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![BU of 5mxd by Molmil](/molmil-images/mine/5mxd) | BACE-1 IN COMPLEX WITH LIGAND 32397778 | Descriptor: | Beta-secretase 1, CHLORIDE ION, ~{N},~{N}-dimethyl-2-pyrrolidin-1-yl-quinazolin-4-amine | Authors: | Alexander, R. | Deposit date: | 2017-01-23 | Release date: | 2018-02-14 | Method: | X-RAY DIFFRACTION (2.52 Å) | Cite: | Human Beta Secretase 1 In Complex With Ligand 32397778 to be published
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3R2F
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![BU of 3r2f by Molmil](/molmil-images/mine/3r2f) | Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with BMS-693391 AKA (2S)-2-((3R)-3-acetamido-3-isobutyl-2-oxo-1-pyrrolidinyl)-N-((1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-2-((2R,4R)-4-propoxy-2-pyrrolidinyl)ethyl)-4-phenylbutanamide | Descriptor: | (2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl}-4-phenylbutanamide, Beta-secretase 1 | Authors: | Muckelbauer, J.K. | Deposit date: | 2011-03-14 | Release date: | 2011-08-31 | Last modified: | 2019-07-17 | Method: | X-RAY DIFFRACTION (2.53 Å) | Cite: | Monosubstituted {gamma}-lactam and conformationally constrained 1,3-diaminopropan-2-ol transition-state isostere inhibitors of {beta}-secretase (BACE). Bioorg.Med.Chem.Lett., 21, 2011
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1W51
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![BU of 1w51 by Molmil](/molmil-images/mine/1w51) | BACE (Beta Secretase) in complex with a nanomolar non-peptidic inhibitor | Descriptor: | 3-[({(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}AMINO)(HYDROXY)METHYL]-N,N-DIPROPYLBENZAMIDE, BETA-SECRETASE 1, IODIDE ION | Authors: | Patel, S, Vuillard, L, Cleasby, A, Murray, C.W, Yon, J. | Deposit date: | 2004-08-04 | Release date: | 2004-09-23 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Apo and Inhibitor Complex Structures of Bace (Beta-Secretase) J.Mol.Biol., 343, 2004
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4X2L
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![BU of 4x2l by Molmil](/molmil-images/mine/4x2l) | Crystal structure of human BACE-1 bound to Compound 6 | Descriptor: | (4S)-4-(2,4-difluorophenyl)-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine, Beta-secretase 1, DIMETHYL SULFOXIDE, ... | Authors: | Vajdos, F.F, Parris, K. | Deposit date: | 2014-11-26 | Release date: | 2015-03-04 | Last modified: | 2017-11-22 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Discovery of a Series of Efficient, Centrally Efficacious BACE1 Inhibitors through Structure-Based Drug Design. J.Med.Chem., 58, 2015
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3TPR
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![BU of 3tpr by Molmil](/molmil-images/mine/3tpr) | Crystal structure of BACE1 complexed with an inhibitor | Descriptor: | Beta-secretase 1, CHLORIDE ION, N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2-HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]-N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE | Authors: | Xu, Y.C, Li, M.J, Greenblatt, H, Chen, T.T, Silman, I, Sussman, J.L. | Deposit date: | 2011-09-08 | Release date: | 2011-11-23 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations Acta Crystallogr.,Sect.D, 68, 2012
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3DM6
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![BU of 3dm6 by Molmil](/molmil-images/mine/3dm6) | Beta-secretase 1 complexed with statine-based inhibitor | Descriptor: | 5-[[(2S)-2-[[(3R,4S)-5-(3,5-difluorophenoxy)-3-hydroxy-4-[[3-(methyl-methylsulfonyl-amino)-5-[[(1R)-1-phenylethyl]carbamoyl]phenyl]carbonylamino]pentanoyl]amino]-3-methyl-butanoyl]amino]benzene-1,3-dicarboxylic acid, Beta-secretase 1, ISOPROPYL ALCOHOL | Authors: | Lindberg, J, Borkakoti, N, Nystrom, S. | Deposit date: | 2008-06-30 | Release date: | 2008-12-16 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues Bioorg.Med.Chem., 16, 2008
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1PY1
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![BU of 1py1 by Molmil](/molmil-images/mine/1py1) | Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide | Descriptor: | ADP-ribosylation factor binding protein GGA1, Beta-secretase | Authors: | Zhu, G, Zhang, X.C. | Deposit date: | 2003-07-07 | Release date: | 2003-11-04 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Biochemical and structural characterization of the interaction of memapsin 2 (beta-secretase)
cytosolic domain with the VHS domain of GGA proteins. Biochemistry, 42, 2003
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3S2O
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![BU of 3s2o by Molmil](/molmil-images/mine/3s2o) | Fragment based discovery and optimisation of bace-1 inhibitors | Descriptor: | (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide, Beta-secretase 1, IODIDE ION | Authors: | Madden, J, Godemann, R, Smith, M.A, Hallett, D, Barker, J, Kraemer, J. | Deposit date: | 2011-05-17 | Release date: | 2011-06-01 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Fragment-based discovery and optimization of BACE1 inhibitors. Bioorg.Med.Chem.Lett., 20, 2010
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1UJJ
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![BU of 1ujj by Molmil](/molmil-images/mine/1ujj) | VHS domain of human GGA1 complexed with C-terminal peptide from BACE | Descriptor: | ADP-ribosylation factor binding protein GGA1, C-terminal peptide from Beta-secretase | Authors: | Shiba, T, Kametaka, S, Kawasaki, M, Shibata, M, Waguri, S, Uchiyama, Y, Wakatsuki, S. | Deposit date: | 2003-08-05 | Release date: | 2004-05-11 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Insights into the Phosphoregulation of beta-Secretase Sorting Signal by the VHS Domain of GGA1 TRAFFIC, 5, 2004
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5QD0
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![BU of 5qd0 by Molmil](/molmil-images/mine/5qd0) | Crystal structure of BACE complex withBMC006 | Descriptor: | (5S,8S,10R)-8-[(1R)-1-hydroxy-2-{[(5-propyl-1H-pyrazol-3-yl)methyl]amino}ethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione, Beta-secretase 1 | Authors: | Rondeau, J.M, Shao, C, Yang, H, Burley, S.K. | Deposit date: | 2017-12-01 | Release date: | 2020-06-03 | Last modified: | 2021-02-10 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J.Comput.Aided Mol.Des., 34, 2020
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2ZJH
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3KYR
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![BU of 3kyr by Molmil](/molmil-images/mine/3kyr) | Bace-1 in complex with a norstatine type inhibitor | Descriptor: | 3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-ylcarbonylamino)propanoyl]amino]-3-methyl-butanoyl]amino]-4-methyl-pentanoyl]amino]methyl]-2-hydroxy-4-phenyl-butanoyl]amino]benzoic acid, Beta-secretase 1 | Authors: | Lindberg, J.D, Borkakoti, N, Derbyshire, D, Nystrom, S. | Deposit date: | 2009-12-07 | Release date: | 2010-12-29 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Investigation of a-phenylnorstatine and a-benzylnorstatine as transition state isostere motifs in the search for new BACE-1 inhibiotrs To be Published
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6JSN
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![BU of 6jsn by Molmil](/molmil-images/mine/6jsn) | Crystal Structure of BACE1 in complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Fujimoto, K, Matsuoka, E, Asada, N, Tadano, G, Yamamoto, T, Nakahara, K, Fuchino, K, Ito, H, Kanegawa, N, Moechars, D, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2019-04-08 | Release date: | 2019-08-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structure-Based Design of Selective beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity over BACE2. J.Med.Chem., 62, 2019
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2QU2
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![BU of 2qu2 by Molmil](/molmil-images/mine/2qu2) | BACE1 with Compound 1 | Descriptor: | Beta-secretase 1, N-[amino(imino)methyl]-2-(2,5-diphenyl-1H-pyrrol-1-yl)acetamide | Authors: | Chopra, R. | Deposit date: | 2007-08-03 | Release date: | 2008-08-05 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Thiophene substituted acylguanidines as BACE1 inhibitors. Bioorg.Med.Chem.Lett., 17, 2007
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5QD9
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![BU of 5qd9 by Molmil](/molmil-images/mine/5qd9) | Crystal structure of BACE complex with BMC005 | Descriptor: | (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl)cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione, Beta-secretase 1 | Authors: | Rondeau, J.M, Shao, C, Yang, H, Burley, S.K. | Deposit date: | 2017-12-01 | Release date: | 2020-06-03 | Last modified: | 2021-02-10 | Method: | X-RAY DIFFRACTION (2.602 Å) | Cite: | D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J.Comput.Aided Mol.Des., 34, 2020
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