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Structure paper

TitleD3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Journal, issue, pagesJ. Comput. Aided Mol. Des., Vol. 34, Page 99-119, Year 2020
Publish dateDec 1, 2017 (structure data deposition date)
AuthorsParks, C.D. / Gaieb, Z. / Chiu, M. / Yang, H. / Shao, C. / Walters, W.P. / Jansen, J.M. / McGaughey, G. / Lewis, R.A. / Bembenek, S.D. ...Parks, C.D. / Gaieb, Z. / Chiu, M. / Yang, H. / Shao, C. / Walters, W.P. / Jansen, J.M. / McGaughey, G. / Lewis, R.A. / Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Burley, S.K. / Amaro, R.E. / Gilson, M.K.
External linksJ. Comput. Aided Mol. Des. / PubMed:31974851
MethodsX-ray diffraction
Resolution1.951 - 2.7 Å
Structure data

PDB-5qco:
Crystal structure of BACE complex with BMC016
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-5qcp:
Crystal structure of BACE complex with BMC018
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-5qcq:
Crystal structure of BACE complex with BMC025
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5qcr:
Crystal structure of BACE complex with BMC026
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-5qcs:
Crystal structure of BACE complex with BMC024
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-5qct:
Crystal structure of BACE complex with BMC001
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-5qcu:
Crystal structure of BACE complex with BMC022
Method: X-RAY DIFFRACTION / Resolution: 1.951 Å

PDB-5qcv:
Crystal structure of BACE complex with BMC023
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-5qcw:
Crystal structure of BACE complex with BMC021
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5qcx:
Crystal structure of BACE complex with BMC007
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-5qcy:
Crystal structure of BACE complex with BMC008
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-5qcz:
Crystal structure of BACE complex with BMC015
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-5qd0:
Crystal structure of BACE complex withBMC006
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-5qd1:
Crystal structure of BACE complex with BMC011
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-5qd2:
Crystal structure of BACE complex with BMC017
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-5qd3:
Crystal structure of BACE complex with BMC010
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

PDB-5qd4:
Crystal structure of BACE complex with BMC023
Method: X-RAY DIFFRACTION / Resolution: 2.112 Å

PDB-5qd5:
Crystal structure of BACE complex with BMC009
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-5qd6:
Crystal structure of BACE complex with BMC004
Method: X-RAY DIFFRACTION / Resolution: 2.51 Å

PDB-5qd7:
Crystal structure of BACE complex with BMC014
Method: X-RAY DIFFRACTION / Resolution: 2.12 Å

PDB-5qd8:
Crystal structure of BACE complex with BMC003
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-5qd9:
Crystal structure of BACE complex with BMC005
Method: X-RAY DIFFRACTION / Resolution: 2.602 Å

PDB-5qda:
Crystal structure of BACE complex with BMC013
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5qdb:
Crystal structure of BACE complex with BMC002
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5qdc:
Crystal structure of BACE complex with BMC019 hydrolyzed
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5qdd:
Crystal structure of BACE complex with BMC020 hydrolyzed
Method: X-RAY DIFFRACTION / Resolution: 2 Å

Chemicals

ChemComp-E4A:
(4S)-19-acetyl-4-[(1R)-1-hydroxy-2-({1-[3-(propan-2-yl)phenyl]cyclopropyl}amino)ethyl]-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one

ChemComp-HOH:
WATER

ChemComp-E4G:
(4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-19-(2-oxopropoxy)-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one

ChemComp-AFJ:
(2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide

ChemComp-E4J:
2-(butylamino)-N-[(2S,3S,5R)-6-(butylamino)-3-hydroxy-5-methyl-6-oxo-1-phenylhexan-2-yl]-6-methoxypyridine-4-carboxamide

ChemComp-SO4:
SULFATE ION

ChemComp-AXF:
(2R,4S)-N-BUTYL-4-HYDROXY-2-METHYL- 4-((E)-(4AS,12R,15S,17AS)-15-METHYL -14,17-DIOXO-2,3,4,4A,6,9,11,12,13, 14,15,16,17,17A-TETRADECAHYDRO-1H-5 ,10-DITHIA-1,13,16-TRIAZA-BENZOCYCL OPENTADECEN-12-YL)-BUTYRAMIDE

ChemComp-E4Y:
(2R,4S)-N-butyl-4-[(4S,6R)-16-ethoxy-12-ethyl-6-methyl-2,13-dioxo-3,12-diazabicyclo[12.3.1]octadeca-1(18),14,16-trien-4-yl]-4-hydroxy-2-methylbutanamide

ChemComp-PO4:
PHOSPHATE ION

ChemComp-E51:
(2R,4S)-N-butyl-4-[(5S,8S,10R)-5,10-dimethyl-3,3,6-trioxo-3lambda~6~-thia-7-azabicyclo[11.3.1]heptadeca-1(17),13,15-trien-8-yl]-4-hydroxy-2-methylbutanamide

ChemComp-E5A:
(10S,13S)-13-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-9,10-dimethyl-2-oxa-9,12-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-8,11-dione

ChemComp-AR9:
(2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide

ChemComp-E5D:
(9R,11S)-3-ethyl-11-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-9-methyl-3,12-diazabicyclo[12.3.1]octadeca-1(18),14,16-triene-2,13-dione

ChemComp-E5P:
(9R,11S)-11-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-9-methyl-16-(1,3-oxazol-2-yl)-3-[(1R)-1-phenylethyl]-3,12-diazabicyclo[12.3.1]octadeca-1(18),14,16-triene-2,13-dione

ChemComp-E5V:
(4S)-4-{(S)-hydroxy[(3R,6R)-6-(methoxymethyl)morpholin-3-yl]methyl}-19-(methoxymethyl)-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one

ChemComp-E5Y:
(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

ChemComp-E61:
(10S,12S)-12-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-17-(methoxymethyl)-10-methyl-7-oxa-2,13-diazabicyclo[13.3.1]nonadeca-1(19),15,17-trien-14-one

ChemComp-E6J:
(4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-19-(methoxymethyl)-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one

ChemComp-E6M:
(10R,12S)-12-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-17-(methoxymethyl)-10-methyl-2,13-diazabicyclo[13.3.1]nonadeca-1(19),15,17-trien-14-one

ChemComp-AXQ:
{(E)-(3R,6S,9R)-3-[(1S,3R)-3-((S)-1 -BUTYLCARBAMOYL-2-METHYL-PROPYLCARB AMOYL)-1-HYDROXY-BUTYL]-6-METHYL-5, 8-DIOXO-1,11-DITHIA-4,7-DIAZA-CYCLO PENTADEC-13-EN-9-YL}-CARBAMIC ACID TERT-BUTYL ESTER

ChemComp-E6P:
(10S,12S)-17-chloro-12-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-10-methyl-7-oxa-2,13,18-triazabicyclo[13.3.1]nonadeca-1(19),15,17-trien-14-one

ChemComp-E6S:
(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

ChemComp-0BI:
(4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl)phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatric

ChemComp-E6V:
(3S,14R,16S)-16-[(1R)-2-{[(4S)-2,2-dimethyl-6-(propan-2-yl)-3,4-dihydro-2H-1-benzopyran-4-yl]amino}-1-hydroxyethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-dione

ChemComp-E6Y:
(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

ChemComp-E74:
(4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-18-methoxy-3,15,17-triazatricyclo[14.3.1.1~6,10~]henicosa-1(20),6(21),7,9,16,18-hexaen-2-one

ChemComp-BAV:
(3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl)benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5-

ChemComp-GOL:
GLYCEROL

ChemComp-E77:
(4S)-4-[(1R)-1,2-dihydroxyethyl]-N,N-dimethyl-2-oxo-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaene-19-carboxamide

ChemComp-E7A:
(10R,12S)-12-[(1R)-1,2-dihydroxyethyl]-N,N,10-trimethyl-14-oxo-2-oxa-13-azabicyclo[13.3.1]nonadeca-1(19),15,17-triene-17-carboxamide

Source
  • homo sapiens (human)
KeywordsHYDROLASE / Hydroloase / D3R / BACE / Ligand Docking

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