data_JB2
# 
_chem_comp.id                                    JB2 
_chem_comp.name                                  GDP-perosamine 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H26 N6 O14 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                        588.357 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     JB2 
_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        4EA7 
_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 
JB2 O6    O6    O 0 1 N N N 45.882 -1.144  17.977 -7.399 -3.653 1.865  O6    JB2 1  
JB2 C6    C6    C 0 1 N N N 45.210 -1.609  17.064 -7.123 -2.905 0.942  C6    JB2 2  
JB2 C5    C5    C 0 1 Y N N 45.173 -2.908  16.647 -6.063 -1.975 1.055  C5    JB2 3  
JB2 N7    N7    N 0 1 Y N N 45.696 -4.086  17.195 -5.178 -1.668 2.034  N7    JB2 4  
JB2 C8    C8    C 0 1 Y N N 45.229 -5.041  16.400 -4.393 -0.715 1.621  C8    JB2 5  
JB2 N1    N1    N 0 1 N N N 44.560 -0.667  16.220 -7.819 -2.948 -0.216 N1    JB2 6  
JB2 C2    C2    C 0 1 N N N 43.899 -1.093  15.065 -7.501 -2.108 -1.241 C2    JB2 7  
JB2 N2    N2    N 0 1 N N N 43.328 -0.089  14.341 -8.225 -2.175 -2.405 N2    JB2 8  
JB2 N3    N3    N 0 1 N N N 43.846 -2.356  14.675 -6.523 -1.236 -1.147 N3    JB2 9  
JB2 C4    C4    C 0 1 Y N N 44.509 -3.240  15.462 -5.787 -1.140 -0.033 C4    JB2 10 
JB2 N9    N9    N 0 1 Y N N 44.535 -4.559  15.297 -4.732 -0.356 0.348  N9    JB2 11 
JB2 "C1'" "C1'" C 0 1 N N R 44.007 -5.309  14.191 -4.084 0.679  -0.461 "C1'" JB2 12 
JB2 "O4'" "O4'" O 0 1 N N N 42.918 -6.094  14.707 -2.733 0.904  -0.003 "O4'" JB2 13 
JB2 "C2'" "C2'" C 0 1 N N R 44.912 -6.383  13.617 -4.797 2.036  -0.268 "C2'" JB2 14 
JB2 "O2'" "O2'" O 0 1 N N N 45.922 -5.783  12.803 -5.713 2.278  -1.339 "O2'" JB2 15 
JB2 "C3'" "C3'" C 0 1 N N S 43.952 -7.320  12.964 -3.649 3.070  -0.289 "C3'" JB2 16 
JB2 "O3'" "O3'" O 0 1 N N N 43.594 -7.030  11.622 -3.818 3.983  -1.376 "O3'" JB2 17 
JB2 "C4'" "C4'" C 0 1 N N R 42.674 -7.197  13.823 -2.379 2.216  -0.493 "C4'" JB2 18 
JB2 "C5'" "C5'" C 0 1 N N N 42.469 -8.374  14.734 -1.215 2.790  0.318  "C5'" JB2 19 
JB2 "O5'" "O5'" O 0 1 N N N 41.954 -9.403  13.841 -0.023 2.057  0.026  "O5'" JB2 20 
JB2 P     P     P 0 1 N N N 41.824 -10.949 14.345 1.399  2.390  0.703  P     JB2 21 
JB2 O1P   O1P   O 0 1 N N N 41.073 -11.674 13.267 1.735  3.813  0.471  O1P   JB2 22 
JB2 O2P   O2P   O 0 1 N N N 43.185 -11.461 14.767 1.318  2.109  2.286  O2P   JB2 23 
JB2 OPP   OPP   O 0 1 N N N 40.924 -10.902 15.705 2.536  1.457  0.049  OPP   JB2 24 
JB2 P2    P2    P 0 1 N N N 39.482 -10.278 15.961 4.146  1.492  0.045  P2    JB2 25 
JB2 O3P   O3P   O 0 1 N N N 39.678 -9.202  16.906 4.655  2.652  -0.948 O3P   JB2 26 
JB2 O4P   O4P   O 0 1 N N N 38.870 -9.900  14.674 4.636  1.763  1.415  O4P   JB2 27 
JB2 O1G   O1G   O 0 1 N N N 38.689 -11.524 16.398 4.712  0.070  -0.456 O1G   JB2 28 
JB2 C1G   C1G   C 0 1 N N R 38.933 -12.321 17.482 6.104  -0.251 -0.471 C1G   JB2 29 
JB2 O5G   O5G   O 0 1 N N N 37.788 -12.033 18.345 6.471  -0.839 0.779  O5G   JB2 30 
JB2 C5G   C5G   C 0 1 N N R 36.547 -12.472 17.928 5.747  -2.029 1.099  C5G   JB2 31 
JB2 C6G   C6G   C 0 1 N N N 35.426 -11.653 18.577 6.201  -2.551 2.464  C6G   JB2 32 
JB2 C2G   C2G   C 0 1 N N S 39.127 -13.772 17.071 6.387  -1.243 -1.602 C2G   JB2 33 
JB2 O2G   O2G   O 0 1 N N N 39.490 -14.484 18.321 7.787  -1.524 -1.652 O2G   JB2 34 
JB2 C3G   C3G   C 0 1 N N S 37.745 -14.311 16.519 5.614  -2.539 -1.340 C3G   JB2 35 
JB2 O3G   O3G   O 0 1 N N N 37.877 -15.804 16.446 5.929  -3.497 -2.352 O3G   JB2 36 
JB2 C4G   C4G   C 0 1 N N S 36.559 -13.919 17.477 6.015  -3.092 0.031  C4G   JB2 37 
JB2 N4A   N4A   N 0 1 N N N 35.353 -14.037 16.576 5.225  -4.294 0.326  N4A   JB2 38 
JB2 H1    H1    H 0 1 N N N 45.375 -6.094  16.592 -3.594 -0.275 2.198  H1    JB2 39 
JB2 H2    H2    H 0 1 N N N 44.576 0.305   16.454 -8.547 -3.581 -0.318 H2    JB2 40 
JB2 H3    H3    H 0 1 N N N 42.851 -0.297  13.487 -8.950 -2.813 -2.490 H3    JB2 41 
JB2 H4    H4    H 0 1 N N N 43.386 0.856   14.664 -8.011 -1.583 -3.144 H4    JB2 42 
JB2 H5    H5    H 0 1 N N N 43.665 -4.640  13.388 -4.086 0.394  -1.513 H5    JB2 43 
JB2 H6    H6    H 0 1 N N N 45.391 -6.908  14.457 -5.317 2.062  0.690  H6    JB2 44 
JB2 H7    H7    H 0 1 N N N 46.462 -5.213  13.337 -6.188 3.117  -1.268 H7    JB2 45 
JB2 H8    H8    H 0 1 N N N 44.334 -8.348  13.045 -3.601 3.607  0.658  H8    JB2 46 
JB2 H9    H9    H 0 1 N N N 42.983 -7.686  11.308 -4.632 4.503  -1.330 H9    JB2 47 
JB2 H10   H10   H 0 1 N N N 41.794 -7.031  13.184 -2.119 2.168  -1.550 H10   JB2 48 
JB2 H11   H11   H 0 1 N N N 43.419 -8.688  15.191 -1.071 3.838  0.054  H11   JB2 49 
JB2 H12   H12   H 0 1 N N N 41.742 -8.138  15.525 -1.439 2.711  1.381  H12   JB2 50 
JB2 H13   H13   H 0 1 N N N 43.405 -12.232 14.258 1.102  1.194  2.513  H13   JB2 51 
JB2 H14   H14   H 0 1 N N N 39.367 -8.388  16.528 4.370  2.539  -1.865 H14   JB2 52 
JB2 H15   H15   H 0 1 N N N 39.849 -11.990 17.993 6.685  0.657  -0.630 H15   JB2 53 
JB2 H16   H16   H 0 1 N N N 36.525 -12.001 16.934 4.680  -1.806 1.132  H16   JB2 54 
JB2 H17   H17   H 0 1 N N N 35.782 -10.630 18.767 6.010  -1.793 3.224  H17   JB2 55 
JB2 H18   H18   H 0 1 N N N 34.558 -11.620 17.902 5.648  -3.458 2.708  H18   JB2 56 
JB2 H19   H19   H 0 1 N N N 35.133 -12.122 19.528 7.267  -2.773 2.431  H19   JB2 57 
JB2 H20   H20   H 0 1 N N N 39.910 -13.868 16.304 6.068  -0.813 -2.552 H20   JB2 58 
JB2 H21   H21   H 0 1 N N N 40.320 -14.154 18.644 8.339  -0.746 -1.811 H21   JB2 59 
JB2 H22   H22   H 0 1 N N N 37.563 -13.891 15.519 4.543  -2.333 -1.351 H22   JB2 60 
JB2 H23   H23   H 0 1 N N N 37.068 -16.178 16.118 5.707  -3.209 -3.249 H23   JB2 61 
JB2 H24   H24   H 0 1 N N N 36.500 -14.611 18.330 7.075  -3.343 0.026  H24   JB2 62 
JB2 H25   H25   H 0 1 N N N 34.528 -13.806 17.091 5.472  -4.677 1.226  H25   JB2 63 
JB2 H26   H26   H 0 1 N N N 35.451 -13.409 15.804 4.236  -4.099 0.275  H26   JB2 64 
# 
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 
JB2 "O3'" "C3'" SING N N 1  
JB2 "O2'" "C2'" SING N N 2  
JB2 "C3'" "C2'" SING N N 3  
JB2 "C3'" "C4'" SING N N 4  
JB2 O1P   P     DOUB N N 5  
JB2 "C2'" "C1'" SING N N 6  
JB2 "C4'" "O4'" SING N N 7  
JB2 "C4'" "C5'" SING N N 8  
JB2 "O5'" P     SING N N 9  
JB2 "O5'" "C5'" SING N N 10 
JB2 "C1'" "O4'" SING N N 11 
JB2 "C1'" N9    SING N N 12 
JB2 N2    C2    SING N N 13 
JB2 P     O2P   SING N N 14 
JB2 P     OPP   SING N N 15 
JB2 O4P   P2    DOUB N N 16 
JB2 N3    C2    DOUB N N 17 
JB2 N3    C4    SING N N 18 
JB2 C2    N1    SING N N 19 
JB2 N9    C4    SING Y N 20 
JB2 N9    C8    SING Y N 21 
JB2 C4    C5    DOUB Y N 22 
JB2 OPP   P2    SING N N 23 
JB2 P2    O1G   SING N N 24 
JB2 P2    O3P   SING N N 25 
JB2 N1    C6    SING N N 26 
JB2 O1G   C1G   SING N N 27 
JB2 C8    N7    DOUB Y N 28 
JB2 O3G   C3G   SING N N 29 
JB2 C3G   C2G   SING N N 30 
JB2 C3G   C4G   SING N N 31 
JB2 N4A   C4G   SING N N 32 
JB2 C5    C6    SING N N 33 
JB2 C5    N7    SING Y N 34 
JB2 C6    O6    DOUB N N 35 
JB2 C2G   C1G   SING N N 36 
JB2 C2G   O2G   SING N N 37 
JB2 C4G   C5G   SING N N 38 
JB2 C1G   O5G   SING N N 39 
JB2 C5G   O5G   SING N N 40 
JB2 C5G   C6G   SING N N 41 
JB2 C8    H1    SING N N 42 
JB2 N1    H2    SING N N 43 
JB2 N2    H3    SING N N 44 
JB2 N2    H4    SING N N 45 
JB2 "C1'" H5    SING N N 46 
JB2 "C2'" H6    SING N N 47 
JB2 "O2'" H7    SING N N 48 
JB2 "C3'" H8    SING N N 49 
JB2 "O3'" H9    SING N N 50 
JB2 "C4'" H10   SING N N 51 
JB2 "C5'" H11   SING N N 52 
JB2 "C5'" H12   SING N N 53 
JB2 O2P   H13   SING N N 54 
JB2 O3P   H14   SING N N 55 
JB2 C1G   H15   SING N N 56 
JB2 C5G   H16   SING N N 57 
JB2 C6G   H17   SING N N 58 
JB2 C6G   H18   SING N N 59 
JB2 C6G   H19   SING N N 60 
JB2 C2G   H20   SING N N 61 
JB2 O2G   H21   SING N N 62 
JB2 C3G   H22   SING N N 63 
JB2 O3G   H23   SING N N 64 
JB2 C4G   H24   SING N N 65 
JB2 N4A   H25   SING N N 66 
JB2 N4A   H26   SING N N 67 
# 
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 
JB2 SMILES           ACDLabs              12.01 "O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(N)C(O)C3O)C)O)O)N" 
JB2 InChI            InChI                1.03  
"InChI=1S/C16H26N6O14P2/c1-4-6(17)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)22-3-19-7-12(22)20-16(18)21-13(7)27/h3-6,8-11,14-15,23-26H,2,17H2,1H3,(H,28,29)(H,30,31)(H3,18,20,21,27)/t4-,5-,6-,8-,9+,10-,11+,14-,15-/m1/s1" 
JB2 InChIKey         InChI                1.03  PMFIPWCEUCAMAY-YVXBHLEUSA-N 
JB2 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]1N" 
JB2 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]1N" 
JB2 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)N" 
JB2 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)N" 
# 
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 
JB2 "SYSTEMATIC NAME" ACDLabs              12.01 
"(2R,3S,4S,5S,6R)-5-amino-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)" 
JB2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4S,5S,6R)-5-azanyl-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 
JB2 "Create component" 2012-03-23 RCSB 
# 
