data_JB3 # _chem_comp.id JB3 _chem_comp.name GDP-N-acetylperosamine _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H28 N6 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-03-23 _chem_comp.pdbx_modified_date 2012-03-30 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 630.394 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JB3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4EA8 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal JB3 O4A O4A O 0 1 N N N -16.884 -35.837 17.364 -6.808 4.179 0.956 O4A JB3 1 JB3 C4A C4A C 0 1 N N N -15.785 -35.237 17.116 -5.768 4.363 0.359 C4A JB3 2 JB3 C5A C5A C 0 1 N N N -15.923 -33.722 16.942 -5.083 5.703 0.434 C5A JB3 3 JB3 N4A N4A N 0 1 N N N -14.497 -35.636 17.025 -5.221 3.367 -0.366 N4A JB3 4 JB3 C4G C4G C 0 1 N N S -14.187 -37.043 17.437 -5.884 2.062 -0.434 C4G JB3 5 JB3 C5G C5G C 0 1 N N R -12.763 -37.100 18.069 -5.469 1.214 0.771 C5G JB3 6 JB3 C6G C6G C 0 1 N N N -12.613 -36.272 19.341 -5.933 1.896 2.059 C6G JB3 7 JB3 O5G O5G O 0 1 N N N -12.343 -38.391 18.228 -6.070 -0.079 0.672 O5G JB3 8 JB3 C3G C3G C 0 1 N N S -14.298 -37.952 16.199 -5.469 1.344 -1.722 C3G JB3 9 JB3 O3G O3G O 0 1 N N N -15.669 -37.939 15.723 -5.918 2.093 -2.853 O3G JB3 10 JB3 C2G C2G C 0 1 N N S -13.861 -39.398 16.587 -6.105 -0.049 -1.744 C2G JB3 11 JB3 O2G O2G O 0 1 N N N -14.771 -40.066 17.522 -7.529 0.076 -1.769 O2G JB3 12 JB3 C1G C1G C 0 1 N N R -12.527 -39.358 17.191 -5.681 -0.816 -0.488 C1G JB3 13 JB3 O1G O1G O 0 1 N N N -11.578 -38.966 16.178 -4.263 -0.987 -0.491 O1G JB3 14 JB3 P2 P2 P 0 1 N N N -10.292 -39.816 15.873 -3.530 -2.247 0.193 P2 JB3 15 JB3 O3P O3P O 0 1 N N N -9.322 -40.024 16.931 -3.942 -3.595 -0.586 O3P JB3 16 JB3 O4P O4P O 0 1 N N N -9.826 -39.229 14.600 -3.946 -2.350 1.610 O4P JB3 17 JB3 OPP OPP O 0 1 N N N -10.911 -41.276 15.590 -1.935 -2.049 0.114 OPP JB3 18 JB3 P P P 0 1 N N N -11.040 -42.134 14.237 -0.683 -2.747 0.848 P JB3 19 JB3 O1P O1P O 0 1 N N N -11.787 -41.309 13.171 -0.870 -4.215 0.852 O1P JB3 20 JB3 O2P O2P O 0 1 N N N -11.601 -43.427 14.647 -0.584 -2.214 2.364 O2P JB3 21 JB3 "O5'" "O5'" O 0 1 N N N -9.542 -42.291 13.781 0.673 -2.381 0.061 "O5'" JB3 22 JB3 "C5'" "C5'" C 0 1 N N N -8.493 -42.791 14.688 1.945 -2.934 0.403 "C5'" JB3 23 JB3 "C4'" "C4'" C 0 1 N N R -7.305 -42.981 13.752 3.014 -2.378 -0.540 "C4'" JB3 24 JB3 "O4'" "O4'" O 0 1 N N N -6.187 -43.203 14.639 3.177 -0.967 -0.316 "O4'" JB3 25 JB3 "C3'" "C3'" C 0 1 N N S -7.403 -44.194 12.841 4.370 -3.049 -0.249 "C3'" JB3 26 JB3 "O3'" "O3'" O 0 1 N N N -7.102 -43.878 11.464 4.847 -3.737 -1.407 "O3'" JB3 27 JB3 "C2'" "C2'" C 0 1 N N R -6.466 -45.234 13.487 5.308 -1.869 0.105 "C2'" JB3 28 JB3 "O2'" "O2'" O 0 1 N N N -5.840 -46.162 12.630 6.598 -2.049 -0.483 "O2'" JB3 29 JB3 "C1'" "C1'" C 0 1 N N R -5.408 -44.282 14.108 4.572 -0.665 -0.535 "C1'" JB3 30 JB3 N9 N9 N 0 1 Y N N -4.631 -44.826 15.213 4.941 0.583 0.138 N9 JB3 31 JB3 C8 C8 C 0 1 Y N N -5.107 -45.477 16.320 4.260 1.183 1.157 C8 JB3 32 JB3 N7 N7 N 0 1 Y N N -4.091 -45.911 17.137 4.871 2.274 1.513 N7 JB3 33 JB3 C4 C4 C 0 1 Y N N -3.289 -44.744 15.397 6.036 1.357 -0.137 C4 JB3 34 JB3 C5 C5 C 0 1 Y N N -2.968 -45.388 16.605 5.976 2.441 0.747 C5 JB3 35 JB3 N3 N3 N 0 1 N N N -2.385 -44.130 14.608 7.045 1.270 -1.012 N3 JB3 36 JB3 C2 C2 C 0 1 N N N -1.131 -44.162 15.024 7.987 2.185 -1.055 C2 JB3 37 JB3 N2 N2 N 0 1 N N N -0.132 -43.627 14.292 9.002 2.053 -1.969 N2 JB3 38 JB3 N1 N1 N 0 1 N N N -0.791 -44.772 16.191 7.986 3.261 -0.218 N1 JB3 39 JB3 C6 C6 C 0 1 N N N -1.641 -45.412 17.000 6.997 3.419 0.689 C6 JB3 40 JB3 O6 O6 O 0 1 N N N -1.238 -46.086 17.970 6.985 4.379 1.440 O6 JB3 41 JB3 H1 H1 H 0 1 N N N -16.977 -33.432 17.068 -5.666 6.374 1.065 H1 JB3 42 JB3 H2 H2 H 0 1 N N N -15.309 -33.209 17.697 -4.087 5.579 0.859 H2 JB3 43 JB3 H3 H3 H 0 1 N N N -15.582 -33.436 15.936 -5.001 6.126 -0.567 H3 JB3 44 JB3 H4 H4 H 0 1 N N N -13.782 -35.019 16.697 -4.390 3.514 -0.843 H4 JB3 45 JB3 H5 H5 H 0 1 N N N -14.919 -37.374 18.189 -6.965 2.201 -0.426 H5 JB3 46 JB3 H6 H6 H 0 1 N N N -12.100 -36.627 17.329 -4.384 1.110 0.785 H6 JB3 47 JB3 H7 H7 H 0 1 N N N -11.585 -36.366 19.721 -7.018 1.999 2.045 H7 JB3 48 JB3 H8 H8 H 0 1 N N N -12.827 -35.216 19.118 -5.637 1.292 2.917 H8 JB3 49 JB3 H9 H9 H 0 1 N N N -13.320 -36.637 20.101 -5.475 2.882 2.134 H9 JB3 50 JB3 H10 H10 H 0 1 N N N -13.621 -37.576 15.417 -4.383 1.249 -1.753 H10 JB3 51 JB3 H11 H11 H 0 1 N N N -16.163 -37.280 16.197 -5.694 1.691 -3.704 H11 JB3 52 JB3 H12 H12 H 0 1 N N N -13.811 -39.989 15.661 -5.771 -0.589 -2.630 H12 JB3 53 JB3 H13 H13 H 0 1 N N N -14.445 -40.938 17.713 -7.998 -0.769 -1.784 H13 JB3 54 JB3 H14 H14 H 0 1 N N N -12.270 -40.359 17.568 -6.166 -1.792 -0.478 H14 JB3 55 JB3 H15 H15 H 0 1 N N N -8.466 -39.734 16.638 -3.700 -3.598 -1.522 H15 JB3 56 JB3 H16 H16 H 0 1 N N N -12.404 -43.591 14.166 -0.460 -1.258 2.437 H16 JB3 57 JB3 H17 H17 H 0 1 N N N -8.790 -43.744 15.151 2.193 -2.667 1.431 H17 JB3 58 JB3 H18 H18 H 0 1 N N N -8.265 -42.056 15.474 1.907 -4.019 0.309 H18 JB3 59 JB3 H19 H19 H 0 1 N N N -7.155 -42.072 13.150 2.724 -2.557 -1.575 H19 JB3 60 JB3 H20 H20 H 0 1 N N N -8.430 -44.584 12.903 4.284 -3.734 0.594 H20 JB3 61 JB3 H21 H21 H 0 1 N N N -7.722 -43.234 11.144 5.724 -4.129 -1.298 H21 JB3 62 JB3 H22 H22 H 0 1 N N N -7.003 -45.748 14.298 5.388 -1.746 1.185 H22 JB3 63 JB3 H23 H23 H 0 1 N N N -5.292 -46.746 13.141 7.061 -2.842 -0.179 H23 JB3 64 JB3 H24 H24 H 0 1 N N N -4.739 -43.922 13.312 4.789 -0.606 -1.602 H24 JB3 65 JB3 H25 H25 H 0 1 N N N -6.156 -45.631 16.526 3.350 0.807 1.601 H25 JB3 66 JB3 H26 H26 H 0 1 N N N -0.333 -43.194 13.413 9.016 1.293 -2.572 H26 JB3 67 JB3 H27 H27 H 0 1 N N N 0.809 -43.664 14.628 9.705 2.721 -2.013 H27 JB3 68 JB3 H28 H28 H 0 1 N N N 0.170 -44.739 16.465 8.697 3.918 -0.276 H28 JB3 69 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal JB3 "O3'" "C3'" SING N N 1 JB3 "O2'" "C2'" SING N N 2 JB3 "C3'" "C2'" SING N N 3 JB3 "C3'" "C4'" SING N N 4 JB3 O1P P DOUB N N 5 JB3 "C2'" "C1'" SING N N 6 JB3 "C4'" "O4'" SING N N 7 JB3 "C4'" "C5'" SING N N 8 JB3 "O5'" P SING N N 9 JB3 "O5'" "C5'" SING N N 10 JB3 "C1'" "O4'" SING N N 11 JB3 "C1'" N9 SING N N 12 JB3 P O2P SING N N 13 JB3 P OPP SING N N 14 JB3 N2 C2 SING N N 15 JB3 O4P P2 DOUB N N 16 JB3 N3 C2 DOUB N N 17 JB3 N3 C4 SING N N 18 JB3 C2 N1 SING N N 19 JB3 N9 C4 SING Y N 20 JB3 N9 C8 SING Y N 21 JB3 C4 C5 DOUB Y N 22 JB3 OPP P2 SING N N 23 JB3 O3G C3G SING N N 24 JB3 P2 O1G SING N N 25 JB3 P2 O3P SING N N 26 JB3 O1G C1G SING N N 27 JB3 N1 C6 SING N N 28 JB3 C3G C2G SING N N 29 JB3 C3G C4G SING N N 30 JB3 C8 N7 DOUB Y N 31 JB3 C2G C1G SING N N 32 JB3 C2G O2G SING N N 33 JB3 C5 C6 SING N N 34 JB3 C5 N7 SING Y N 35 JB3 C5A C4A SING N N 36 JB3 C6 O6 DOUB N N 37 JB3 N4A C4A SING N N 38 JB3 N4A C4G SING N N 39 JB3 C4A O4A DOUB N N 40 JB3 C1G O5G SING N N 41 JB3 C4G C5G SING N N 42 JB3 C5G O5G SING N N 43 JB3 C5G C6G SING N N 44 JB3 C5A H1 SING N N 45 JB3 C5A H2 SING N N 46 JB3 C5A H3 SING N N 47 JB3 N4A H4 SING N N 48 JB3 C4G H5 SING N N 49 JB3 C5G H6 SING N N 50 JB3 C6G H7 SING N N 51 JB3 C6G H8 SING N N 52 JB3 C6G H9 SING N N 53 JB3 C3G H10 SING N N 54 JB3 O3G H11 SING N N 55 JB3 C2G H12 SING N N 56 JB3 O2G H13 SING N N 57 JB3 C1G H14 SING N N 58 JB3 O3P H15 SING N N 59 JB3 O2P H16 SING N N 60 JB3 "C5'" H17 SING N N 61 JB3 "C5'" H18 SING N N 62 JB3 "C4'" H19 SING N N 63 JB3 "C3'" H20 SING N N 64 JB3 "O3'" H21 SING N N 65 JB3 "C2'" H22 SING N N 66 JB3 "O2'" H23 SING N N 67 JB3 "C1'" H24 SING N N 68 JB3 C8 H25 SING N N 69 JB3 N2 H26 SING N N 70 JB3 N2 H27 SING N N 71 JB3 N1 H28 SING N N 72 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor JB3 SMILES ACDLabs 12.01 "O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(NC(=O)C)C(O)C3O)C)O)O)N" JB3 InChI InChI 1.03 ;InChI=1S/C18H28N6O15P2/c1-5-8(21-6(2)25)11(27)13(29)17(36-5)38-41(33,34)39-40(31,32)35-3-7-10(26)12(28)16(37-7)24-4-20-9-14(24)22-18(19)23-15(9)30/h4-5,7-8,10-13,16-17,26-29H,3H2,1-2H3,(H,21,25)(H,31,32)(H,33,34)(H3,19,22,23,30)/t5-,7-,8-,10-,11+,12-,13+,16-,17-/m1/s1 ; JB3 InChIKey InChI 1.03 QYYLCPNKZRMSFL-XEDXKBCUSA-N JB3 SMILES_CANONICAL CACTVS 3.370 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)[C@@H]1NC(C)=O" JB3 SMILES CACTVS 3.370 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)[CH]1NC(C)=O" JB3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)NC(=O)C" JB3 SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)NC(=O)C" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier JB3 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3S,4S,5S,6R)-5-(acetylamino)-3,4-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" JB3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4S,5S,6R)-5-acetamido-6-methyl-3,4-bis(oxidanyl)oxan-2-yl] [[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site JB3 "Create component" 2012-03-23 RCSB #