data_YLB # _chem_comp.id YLB _chem_comp.name "5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H32 N7 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-28 _chem_comp.pdbx_modified_date 2014-03-14 _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 545.483 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YLB _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 4CH3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 YLB C C C 0 1 N N N 42.970 133.810 -11.193 2.305 -2.116 -1.471 C YLB 1 YLB N N N 0 1 N N N 43.897 136.000 -11.154 4.099 -1.907 -3.096 N YLB 2 YLB O O O 0 1 N N N 42.052 133.827 -11.992 2.251 -3.283 -1.776 O YLB 3 YLB N1 N1 N 0 1 Y N N 36.047 126.091 -11.750 -8.586 3.462 -0.449 N1 YLB 4 YLB C2 C2 C 0 1 Y N N 36.216 126.145 -10.405 -8.237 3.129 0.780 C2 YLB 5 YLB C3 C3 C 0 1 N N N 44.606 143.198 -8.231 12.894 3.136 2.203 C3 YLB 6 YLB N3 N3 N 0 1 Y N N 37.194 126.863 -9.805 -7.238 2.311 1.034 N3 YLB 7 YLB C4 C4 C 0 1 Y N N 38.052 127.587 -10.577 -6.528 1.780 0.043 C4 YLB 8 YLB C5 C5 C 0 1 Y N N 37.932 127.582 -12.055 -6.860 2.103 -1.283 C5 YLB 9 YLB C6 C6 C 0 1 Y N N 36.840 126.762 -12.625 -7.935 2.980 -1.503 C6 YLB 10 YLB N6 N6 N 0 1 N N N 36.651 126.691 -13.960 -8.309 3.335 -2.788 N6 YLB 11 YLB N7 N7 N 0 1 Y N N 38.912 128.369 -12.543 -5.994 1.438 -2.085 N7 YLB 12 YLB C8 C8 C 0 1 Y N N 39.611 128.849 -11.474 -5.172 0.744 -1.352 C8 YLB 13 YLB N9 N9 N 0 1 Y N N 39.093 128.367 -10.305 -5.460 0.922 -0.032 N9 YLB 14 YLB CA CA C 0 1 N N R 43.226 135.008 -10.327 3.459 -1.267 -1.939 CA YLB 15 YLB CB CB C 0 1 N N N 43.978 134.598 -9.039 4.478 -1.122 -0.807 CB YLB 16 YLB "C1'" "C1'" C 0 1 N N R 39.519 128.656 -8.922 -4.759 0.309 1.099 "C1'" YLB 17 YLB "C2'" "C2'" C 0 1 N N R 40.580 127.722 -8.438 -5.482 -0.984 1.554 "C2'" YLB 18 YLB "O2'" "O2'" O 0 1 N N N 40.433 127.592 -7.023 -6.522 -0.685 2.488 "O2'" YLB 19 YLB "C3'" "C3'" C 0 1 N N S 41.863 128.458 -8.755 -4.338 -1.773 2.235 "C3'" YLB 20 YLB "O3'" "O3'" O 0 1 N N N 42.989 128.053 -7.983 -4.378 -1.590 3.652 "O3'" YLB 21 YLB "C4'" "C4'" C 0 1 N N R 41.452 129.862 -8.397 -3.053 -1.157 1.648 "C4'" YLB 22 YLB "O4'" "O4'" O 0 1 N N N 40.092 129.961 -8.859 -3.454 -0.159 0.695 "O4'" YLB 23 YLB "C5'" "C5'" C 0 1 N N N 42.366 130.885 -9.032 -2.228 -2.240 0.951 "C5'" YLB 24 YLB "O5'" "O5'" O 0 1 N N N 42.155 130.859 -10.428 -0.986 -1.685 0.512 "O5'" YLB 25 YLB OAD OAD O 0 1 N N N 44.961 139.381 -6.227 9.918 2.495 -0.650 OAD YLB 26 YLB OAF OAF O 0 1 N N N 42.821 131.166 -12.807 -0.470 -3.175 -1.459 OAF YLB 27 YLB OAI OAI O 0 1 N N N 44.528 130.273 -11.060 0.707 -3.686 0.715 OAI YLB 28 YLB CAM CAM C 0 1 N N N 45.149 136.289 -7.616 6.606 -0.016 -0.107 CAM YLB 29 YLB CAN CAN C 0 1 N N N 45.316 135.296 -8.762 5.587 -0.161 -1.239 CAN YLB 30 YLB CAO CAO C 0 1 N N N 46.299 137.271 -7.530 7.715 0.946 -0.539 CAO YLB 31 YLB NAW NAW N 0 1 N N N 45.923 138.548 -8.105 8.691 1.084 0.544 NAW YLB 32 YLB OAY OAY O 0 1 N N N 43.831 132.643 -11.073 1.335 -1.573 -0.718 OAY YLB 33 YLB CBA CBA C 0 1 N N N 45.276 139.496 -7.416 9.762 1.887 0.388 CBA YLB 34 YLB CBF CBF C 0 1 N N N 44.853 141.986 -7.360 11.875 2.991 1.071 CBF YLB 35 YLB CBK CBK C 0 1 N N N 44.939 140.737 -8.227 10.766 2.030 1.503 CBK YLB 36 YLB PBN PBN P 0 1 N N N 43.356 131.161 -11.425 0.133 -2.544 -0.264 PBN YLB 37 YLB HN HN H 0 1 N N N 44.085 136.817 -10.609 4.448 -2.823 -2.855 HN YLB 38 YLB HNA HNA H 0 1 N N N 44.757 135.622 -11.496 3.465 -1.956 -3.879 HNA YLB 39 YLB H2 H2 H 0 1 N N N 35.535 125.586 -9.781 -8.793 3.543 1.609 H2 YLB 40 YLB H3 H3 H 0 1 N N N 44.545 144.097 -7.600 13.684 3.821 1.895 H3 YLB 41 YLB H3A H3A H 0 1 N N N 45.433 143.309 -8.948 12.398 3.529 3.091 H3A YLB 42 YLB H3B H3B H 0 1 N N N 43.661 143.069 -8.779 13.326 2.161 2.429 H3B YLB 43 YLB HN6 HN6 H 0 1 N N N 35.873 126.094 -14.156 -9.053 3.941 -2.927 HN6 YLB 44 YLB HN6A HN6A H 0 0 N N N 36.467 127.606 -14.320 -7.826 2.977 -3.549 HN6A YLB 45 YLB H8 H8 H 0 1 N N N 40.457 129.517 -11.542 -4.378 0.119 -1.734 H8 YLB 46 YLB HA HA H 0 1 N N N 42.251 135.415 -10.020 3.092 -0.282 -2.226 HA YLB 47 YLB HB HB H 0 1 N N N 43.314 134.804 -8.187 3.982 -0.730 0.080 HB YLB 48 YLB HBA HBA H 0 1 N N N 44.174 133.517 -9.099 4.910 -2.097 -0.581 HBA YLB 49 YLB "H1'" "H1'" H 0 1 N N N 38.649 128.593 -8.251 -4.677 1.015 1.926 "H1'" YLB 50 YLB "H2'" "H2'" H 0 1 N N N 40.535 126.754 -8.959 -5.877 -1.531 0.697 "H2'" YLB 51 YLB "HO2'" "HO2'" H 0 0 N N N 41.098 127.001 -6.688 -7.003 -1.463 2.802 "HO2'" YLB 52 YLB "H3'" "H3'" H 0 1 N N N 42.076 128.392 -9.832 -4.403 -2.832 1.986 "H3'" YLB 53 YLB "HO3'" "HO3'" H 0 0 N N N 43.750 128.560 -8.242 -5.192 -1.908 4.066 "HO3'" YLB 54 YLB "H4'" "H4'" H 0 1 N N N 41.487 129.979 -7.304 -2.466 -0.696 2.443 "H4'" YLB 55 YLB "H5'" "H5'" H 0 1 N N N 42.135 131.886 -8.639 -2.035 -3.055 1.648 "H5'" YLB 56 YLB "H5'A" "H5'A" H 0 0 N N N 43.414 130.637 -8.809 -2.780 -2.620 0.091 "H5'A" YLB 57 YLB HAM HAM H 0 1 N N N 44.216 136.851 -7.769 6.110 0.377 0.780 HAM YLB 58 YLB HAMA HAMA H 0 0 N N N 45.090 135.730 -6.670 7.038 -0.991 0.119 HAMA YLB 59 YLB HAN HAN H 0 1 N N N 46.071 134.544 -8.488 6.083 -0.553 -2.127 HAN YLB 60 YLB HANA HANA H 0 0 N N N 45.643 135.832 -9.665 5.155 0.814 -1.466 HANA YLB 61 YLB HAO HAO H 0 1 N N N 46.572 137.416 -6.474 8.211 0.553 -1.427 HAO YLB 62 YLB HAOA HAOA H 0 0 N N N 47.162 136.867 -8.080 7.283 1.920 -0.766 HAOA YLB 63 YLB HNAW HNAW H 0 0 N N N 46.158 138.729 -9.060 8.566 0.598 1.375 HNAW YLB 64 YLB HBF HBF H 0 1 N N N 45.798 142.116 -6.812 11.443 3.966 0.845 HBF YLB 65 YLB HBFA HBFA H 0 0 N N N 44.026 141.877 -6.643 12.371 2.599 0.183 HBFA YLB 66 YLB HBK HBK H 0 1 N N N 45.720 140.886 -8.987 10.270 2.422 2.391 HBK YLB 67 YLB HBKA HBKA H 0 0 N N N 43.970 140.583 -8.723 11.198 1.055 1.729 HBKA YLB 68 YLB HAI HAI H 0 1 N N N 44.805 129.783 -11.825 1.118 -3.343 1.521 HAI YLB 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 YLB C O DOUB N N 1 YLB C CA SING N N 2 YLB C OAY SING N N 3 YLB N CA SING N N 4 YLB N1 C2 DOUB Y N 5 YLB N1 C6 SING Y N 6 YLB C2 N3 SING Y N 7 YLB C3 CBF SING N N 8 YLB N3 C4 DOUB Y N 9 YLB C4 C5 SING Y N 10 YLB C4 N9 SING Y N 11 YLB C5 C6 DOUB Y N 12 YLB C5 N7 SING Y N 13 YLB C6 N6 SING N N 14 YLB N7 C8 DOUB Y N 15 YLB C8 N9 SING Y N 16 YLB N9 "C1'" SING N N 17 YLB CA CB SING N N 18 YLB CB CAN SING N N 19 YLB "C1'" "C2'" SING N N 20 YLB "C1'" "O4'" SING N N 21 YLB "C2'" "O2'" SING N N 22 YLB "C2'" "C3'" SING N N 23 YLB "C3'" "O3'" SING N N 24 YLB "C3'" "C4'" SING N N 25 YLB "C4'" "O4'" SING N N 26 YLB "C4'" "C5'" SING N N 27 YLB "C5'" "O5'" SING N N 28 YLB "O5'" PBN SING N N 29 YLB OAD CBA DOUB N N 30 YLB OAF PBN DOUB N N 31 YLB OAI PBN SING N N 32 YLB CAM CAN SING N N 33 YLB CAM CAO SING N N 34 YLB CAO NAW SING N N 35 YLB NAW CBA SING N N 36 YLB OAY PBN SING N N 37 YLB CBA CBK SING N N 38 YLB CBF CBK SING N N 39 YLB N HN SING N N 40 YLB N HNA SING N N 41 YLB C2 H2 SING N N 42 YLB C3 H3 SING N N 43 YLB C3 H3A SING N N 44 YLB C3 H3B SING N N 45 YLB N6 HN6 SING N N 46 YLB N6 HN6A SING N N 47 YLB C8 H8 SING N N 48 YLB CA HA SING N N 49 YLB CB HB SING N N 50 YLB CB HBA SING N N 51 YLB "C1'" "H1'" SING N N 52 YLB "C2'" "H2'" SING N N 53 YLB "O2'" "HO2'" SING N N 54 YLB "C3'" "H3'" SING N N 55 YLB "O3'" "HO3'" SING N N 56 YLB "C4'" "H4'" SING N N 57 YLB "C5'" "H5'" SING N N 58 YLB "C5'" "H5'A" SING N N 59 YLB CAM HAM SING N N 60 YLB CAM HAMA SING N N 61 YLB CAN HAN SING N N 62 YLB CAN HANA SING N N 63 YLB CAO HAO SING N N 64 YLB CAO HAOA SING N N 65 YLB NAW HNAW SING N N 66 YLB CBF HBF SING N N 67 YLB CBF HBFA SING N N 68 YLB CBK HBK SING N N 69 YLB CBK HBKA SING N N 70 YLB OAI HAI SING N N 71 # 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 YLB SMILES ACDLabs 12.01 "O=C(NCCCCC(N)C(=O)OP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)CCC" YLB InChI InChI 1.03 "InChI=1S/C20H32N7O9P/c1-2-5-13(28)23-7-4-3-6-11(21)20(31)36-37(32,33)34-8-12-15(29)16(30)19(35-12)27-10-26-14-17(22)24-9-25-18(14)27/h9-12,15-16,19,29-30H,2-8,21H2,1H3,(H,23,28)(H,32,33)(H2,22,24,25)/p-1/t11-,12-,15-,16-,19-/m1/s1" YLB InChIKey InChI 1.03 OAECZBFMQNITMX-JCQVVMGJSA-M YLB SMILES_CANONICAL CACTVS 3.385 "CCCC(=O)NCCCC[C@@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" YLB SMILES CACTVS 3.385 "CCCC(=O)NCCCC[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" YLB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCC(=O)NCCCC[C@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N" YLB SMILES "OpenEye OEToolkits" 1.7.6 "CCCC(=O)NCCCCC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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 YLB "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-({[(2R)-2-amino-6-(butanoylamino)hexanoyl]oxy}phosphinato)adenosine" YLB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2R)-2-azanyl-6-(butanoylamino)hexanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YLB "Create component" 2013-11-28 EBI YLB "Initial release" 2014-03-19 RCSB #