data_RBY # _chem_comp.id RBY _chem_comp.name "METHYLENE ADP-BETA-XYLOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N5 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-07-27 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 557.343 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RBY _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 2YVP _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 RBY PA PA P 0 1 N N R 11.435 31.554 62.078 -0.682 1.870 -0.561 PA RBY 1 RBY "O5'" O5* O 0 1 N N N 11.647 32.901 61.141 0.716 1.678 0.214 "O5'" RBY 2 RBY "C5'" C5* C 0 1 N N N 11.164 33.698 60.109 1.905 2.388 -0.138 "C5'" RBY 3 RBY "C4'" C4* C 0 1 N N R 12.503 34.587 60.232 3.044 1.970 0.794 "C4'" RBY 4 RBY "O4'" O4* O 0 1 N N N 13.164 34.942 61.546 3.383 0.592 0.565 "O4'" RBY 5 RBY "C3'" C3* C 0 1 N N S 13.751 35.012 59.314 4.302 2.807 0.493 "C3'" RBY 6 RBY "O3'" O3* O 0 1 N N N 13.475 35.493 58.132 4.698 3.548 1.649 "O3'" RBY 7 RBY "C2'" C2* C 0 1 N N R 14.843 35.893 60.173 5.379 1.757 0.127 "C2'" RBY 8 RBY "O2'" O2* O 0 1 N N N 15.463 36.982 59.572 6.641 2.098 0.704 "O2'" RBY 9 RBY "C1'" C1* C 0 1 N N R 14.070 36.257 61.437 4.806 0.468 0.771 "C1'" RBY 10 RBY N9 N9 N 0 1 Y N N 14.925 36.294 62.515 5.325 -0.722 0.092 N9 RBY 11 RBY C8 C8 C 0 1 Y N N 15.121 35.150 63.288 4.716 -1.401 -0.922 C8 RBY 12 RBY N7 N7 N 0 1 Y N N 15.985 35.414 64.217 5.455 -2.407 -1.289 N7 RBY 13 RBY C5 C5 C 0 1 Y N N 16.370 36.719 64.097 6.581 -2.438 -0.537 C5 RBY 14 RBY C6 C6 C 0 1 Y N N 17.278 37.567 64.807 7.711 -3.272 -0.483 C6 RBY 15 RBY N6 N6 N 0 1 N N N 18.008 37.122 65.847 7.836 -4.351 -1.339 N6 RBY 16 RBY N1 N1 N 0 1 Y N N 17.431 38.825 64.443 8.658 -2.999 0.410 N1 RBY 17 RBY C2 C2 C 0 1 Y N N 16.773 39.379 63.419 8.547 -1.970 1.231 C2 RBY 18 RBY N3 N3 N 0 1 Y N N 15.909 38.665 62.683 7.507 -1.163 1.216 N3 RBY 19 RBY C4 C4 C 0 1 Y N N 15.686 37.320 63.000 6.514 -1.354 0.354 C4 RBY 20 RBY CX CX C 0 1 N N N 12.674 31.563 63.009 -1.905 0.686 0.090 CX RBY 21 RBY PB PB P 0 1 N N S 13.867 30.267 63.536 -3.489 0.904 -0.786 PB RBY 22 RBY O1B O1B O 0 1 N N N 14.750 31.498 62.754 -3.289 0.662 -2.233 O1B RBY 23 RBY OR5 OR5 O 0 1 N N N 14.204 30.292 64.921 -4.569 -0.142 -0.212 OR5 RBY 24 RBY CR5 CR5 C 0 1 N N N 13.801 29.618 66.081 -5.878 -0.292 -0.765 CR5 RBY 25 RBY CR4 CR4 C 0 1 N N S 14.589 30.221 67.090 -6.641 -1.365 0.014 CR4 RBY 26 RBY OR4 OR4 O 0 1 N N N 15.761 30.538 67.703 -6.955 -0.894 1.343 OR4 RBY 27 RBY CR3 CR3 C 0 1 N N S 13.517 31.120 67.399 -8.013 -1.633 -0.643 CR3 RBY 28 RBY OR3 OR3 O 0 1 N N N 12.292 31.380 66.927 -8.437 -0.497 -1.399 OR3 RBY 29 RBY CR2 CR2 C 0 1 N N R 13.948 32.030 68.412 -8.962 -1.872 0.553 CR2 RBY 30 RBY OR2 OR2 O 0 1 N N N 13.046 32.231 69.547 -9.516 -3.188 0.497 OR2 RBY 31 RBY CR1 CR1 C 0 1 N N R 15.406 31.569 68.683 -8.051 -1.720 1.791 CR1 RBY 32 RBY OR1 OR1 O 0 1 N N N 16.269 32.693 68.471 -8.759 -1.076 2.852 OR1 RBY 33 RBY O2A O2A O 0 1 N N N 11.336 30.234 61.145 -0.482 1.628 -2.007 O2A RBY 34 RBY O2B O2B O 0 1 N N N 14.005 28.815 62.759 -4.024 2.406 -0.562 O2B RBY 35 RBY O1A O1A O 0 1 N N N 10.227 31.710 63.094 -1.217 3.372 -0.336 O1A RBY 36 RBY "H5'1" 1H5* H 0 0 N N N 10.204 34.209 60.274 2.175 2.155 -1.168 "H5'1" RBY 37 RBY "H5'2" 2H5* H 0 0 N N N 10.861 33.259 59.147 1.731 3.459 -0.041 "H5'2" RBY 38 RBY "H4'" H4* H 0 1 N N N 11.556 34.716 59.687 2.743 2.110 1.832 "H4'" RBY 39 RBY "H3'" H3* H 0 1 N N N 14.232 34.063 59.035 4.122 3.477 -0.348 "H3'" RBY 40 RBY "HO3'" HO3* H 0 0 N N N 13.408 36.439 58.182 5.518 4.048 1.533 "HO3'" RBY 41 RBY "H2'" H2* H 0 1 N N N 15.747 35.286 60.330 5.464 1.647 -0.954 "H2'" RBY 42 RBY "HO2'" HO2* H 0 0 N N N 15.604 37.663 60.219 6.997 2.943 0.399 "HO2'" RBY 43 RBY "H1'" H1* H 0 1 N N N 13.545 37.223 61.416 5.039 0.435 1.836 "H1'" RBY 44 RBY H8 H8 H 0 1 N N N 14.632 34.199 63.137 3.762 -1.142 -1.356 H8 RBY 45 RBY HN61 1HN6 H 0 0 N N N 18.961 37.012 65.563 7.139 -4.540 -1.987 HN61 RBY 46 RBY HN62 2HN6 H 0 0 N N N 17.958 37.783 66.596 8.621 -4.919 -1.293 HN62 RBY 47 RBY H2 H2 H 0 1 N N N 16.940 40.419 63.181 9.339 -1.785 1.941 H2 RBY 48 RBY HX1 1HX H 0 1 N N N 13.330 32.295 62.515 -1.543 -0.331 -0.061 HX1 RBY 49 RBY HX2 2HX H 0 1 N N N 12.120 31.620 63.958 -2.053 0.864 1.156 HX2 RBY 50 RBY HR51 1HR5 H 0 0 N N N 12.726 29.747 66.273 -6.412 0.655 -0.697 HR51 RBY 51 RBY HR52 2HR5 H 0 0 N N N 13.942 28.529 66.017 -5.799 -0.590 -1.811 HR52 RBY 52 RBY HOR3 HOR3 H 0 0 N N N 11.680 31.442 67.651 -9.293 -0.611 -1.834 HOR3 RBY 53 RBY HR2 HR2 H 0 1 N N N 13.921 33.083 68.094 -9.755 -1.124 0.567 HR2 RBY 54 RBY HOR2 HOR2 H 0 0 N N N 13.552 32.275 70.350 -10.120 -3.392 1.225 HOR2 RBY 55 RBY HR1 HR1 H 0 1 N N N 15.504 31.178 69.707 -7.685 -2.694 2.115 HR1 RBY 56 RBY HOR1 HOR1 H 0 0 N N N 16.460 33.108 69.304 -8.221 -0.910 3.639 HOR1 RBY 57 RBY HO2B HO2B H 0 0 N N N 14.031 28.959 61.820 -4.177 2.634 0.365 HO2B RBY 58 RBY HO1A HO1A H 0 0 N N N 10.562 31.741 63.982 -1.371 3.601 0.591 HO1A RBY 59 RBY HR3 HR3 H 0 1 N N N 12.992 30.325 66.850 -7.966 -2.519 -1.276 HR3 RBY 60 RBY HR4 HR4 H 0 1 N N N 15.372 29.453 67.172 -6.058 -2.284 0.064 HR4 RBY 61 # 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 RBY "O3'" "C3'" SING N N 1 RBY "C3'" "C2'" SING N N 2 RBY "C3'" "C4'" SING N N 3 RBY "O2'" "C2'" SING N N 4 RBY "C5'" "C4'" SING N N 5 RBY "C5'" "O5'" SING N N 6 RBY "C2'" "C1'" SING N N 7 RBY "C4'" "O4'" SING N N 8 RBY "O5'" PA SING N N 9 RBY O2A PA DOUB N N 10 RBY "C1'" "O4'" SING N N 11 RBY "C1'" N9 SING N N 12 RBY PA CX SING N N 13 RBY PA O1A SING N N 14 RBY N9 C4 SING Y N 15 RBY N9 C8 SING Y N 16 RBY N3 C4 DOUB Y N 17 RBY N3 C2 SING Y N 18 RBY O1B PB DOUB N N 19 RBY O2B PB SING N N 20 RBY C4 C5 SING Y N 21 RBY CX PB SING N N 22 RBY C8 N7 DOUB Y N 23 RBY C2 N1 DOUB Y N 24 RBY PB OR5 SING N N 25 RBY C5 N7 SING Y N 26 RBY C5 C6 DOUB Y N 27 RBY N1 C6 SING Y N 28 RBY C6 N6 SING N N 29 RBY OR5 CR5 SING N N 30 RBY CR5 CR4 SING N N 31 RBY OR3 CR3 SING N N 32 RBY CR4 CR3 SING N N 33 RBY CR4 OR4 SING N N 34 RBY CR3 CR2 SING N N 35 RBY OR4 CR1 SING N N 36 RBY CR2 CR1 SING N N 37 RBY CR2 OR2 SING N N 38 RBY OR1 CR1 SING N N 39 RBY "C5'" "H5'1" SING N N 40 RBY "C5'" "H5'2" SING N N 41 RBY "C4'" "H4'" SING N N 42 RBY "C3'" "H3'" SING N N 43 RBY "O3'" "HO3'" SING N N 44 RBY "C2'" "H2'" SING N N 45 RBY "O2'" "HO2'" SING N N 46 RBY "C1'" "H1'" SING N N 47 RBY C8 H8 SING N N 48 RBY N6 HN61 SING N N 49 RBY N6 HN62 SING N N 50 RBY C2 H2 SING N N 51 RBY CX HX1 SING N N 52 RBY CX HX2 SING N N 53 RBY CR5 HR51 SING N N 54 RBY CR5 HR52 SING N N 55 RBY OR3 HOR3 SING N N 56 RBY CR2 HR2 SING N N 57 RBY OR2 HOR2 SING N N 58 RBY CR1 HR1 SING N N 59 RBY OR1 HOR1 SING N N 60 RBY O2B HO2B SING N N 61 RBY O1A HO1A SING N N 62 RBY CR3 HR3 SING N N 63 RBY CR4 HR4 SING N N 64 # 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 RBY SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC4OC(O)C(O)C4O" RBY SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H]3O" RBY SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O" RBY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OCC4C([C@H]([C@@H](O4)O)O)O)O)O)O)N" RBY SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)O)N" RBY InChI InChI 1.03 "InChI=1S/C16H25N5O13P2/c17-13-8-14(19-3-18-13)21(4-20-8)15-11(24)9(22)6(33-15)1-31-35(27,28)5-36(29,30)32-2-7-10(23)12(25)16(26)34-7/h3-4,6-7,9-12,15-16,22-26H,1-2,5H2,(H,27,28)(H,29,30)(H2,17,18,19)/t6-,7-,9-,10+,11-,12-,15-,16-/m1/s1" RBY InChIKey InChI 1.03 ZPZRETFSCSWNDT-CAUCCWOKSA-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 RBY "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl methanediylbis[hydrogen (S,R)-phosphonate] (non-preferred name)" RBY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[hydroxy-[[(4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl]methyl]phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RBY "Create component" 2007-07-27 RCSB RBY "Modify aromatic_flag" 2011-06-04 RCSB RBY "Modify descriptor" 2011-06-04 RCSB #