data_1YD # _chem_comp.id 1YD _chem_comp.name "2-amino-9-[(2R,3R,3aR,5S,7aS,9R,10R,10aR,12R,14aS)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H24 N10 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-08-02 _chem_comp.pdbx_modified_date 2013-08-09 _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 674.411 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1YD _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 4LOK _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 1YD OAC OAC O 0 1 N N N 17.823 4.947 24.152 9.261 -2.670 -1.631 OAC 1YD 1 1YD CBC CBC C 0 1 N N N 16.958 4.111 24.343 8.705 -1.816 -0.962 CBC 1YD 2 1YD NAT NAT N 0 1 N N N 15.803 4.554 24.909 9.407 -0.800 -0.413 NAT 1YD 3 1YD CBA CBA C 0 1 N N N 14.810 3.650 25.140 8.775 0.150 0.333 CBA 1YD 4 1YD NAA NAA N 0 1 N N N 13.715 4.111 25.714 9.514 1.170 0.878 NAA 1YD 5 1YD NAS NAS N 0 1 N N N 14.980 2.362 24.815 7.478 0.117 0.545 NAS 1YD 6 1YD CBG CBG C 0 1 Y N N 16.126 1.965 24.260 6.718 -0.858 0.033 CBG 1YD 7 1YD CBE CBE C 0 1 Y N N 17.108 2.833 24.029 7.308 -1.860 -0.746 CBE 1YD 8 1YD NAR NAR N 0 1 Y N N 18.107 2.171 23.482 6.320 -2.705 -1.129 NAR 1YD 9 1YD CAL CAL C 0 1 Y N N 17.754 0.906 23.374 5.186 -2.291 -0.643 CAL 1YD 10 1YD NBQ NBQ N 0 1 Y N N 16.530 0.772 23.856 5.382 -1.150 0.079 NBQ 1YD 11 1YD CBO CBO C 0 1 N N R 15.697 -0.446 23.938 4.351 -0.382 0.782 CBO 1YD 12 1YD CBI CBI C 0 1 N N R 14.796 -0.645 22.667 3.847 0.759 -0.116 CBI 1YD 13 1YD OAG OAG O 0 1 N N N 13.538 -1.175 23.058 4.421 2.004 0.287 OAG 1YD 14 1YD OAX OAX O 0 1 N N N 16.518 -1.596 23.933 3.237 -1.221 1.076 OAX 1YD 15 1YD CBK CBK C 0 1 N N S 16.799 -1.607 22.591 2.005 -0.581 0.763 CBK 1YD 16 1YD CAN CAN C 0 1 N N N 17.827 -2.622 22.202 1.192 -0.356 2.041 CAN 1YD 17 1YD OAV OAV O 0 1 N N N 18.867 -1.774 21.785 -0.089 -0.975 1.904 OAV 1YD 18 1YD PBR PBR P 0 1 N N N 20.209 -2.248 21.150 -1.456 -0.279 2.393 PBR 1YD 19 1YD "O3'" O3* O 0 1 N N N 19.850 -2.624 19.626 -2.475 -0.167 1.152 "O3'" 1YD 20 1YD OAH OAH O 0 1 N N N 21.030 -0.939 21.274 -2.070 -1.097 3.464 OAH 1YD 21 1YD OAD OAD O 0 1 N N N 20.755 -3.439 21.790 -1.136 1.194 2.959 OAD 1YD 22 1YD CBM CBM C 0 1 N N R 15.440 -1.777 21.962 2.324 0.771 0.106 CBM 1YD 23 1YD OAZ OAZ O 0 1 N N N 15.590 -1.709 20.530 1.640 0.891 -1.143 OAZ 1YD 24 1YD PBS PBS P 0 1 N N N 15.037 -0.795 19.387 0.742 2.170 -1.531 PBS 1YD 25 1YD OAI OAI O 0 1 N N N 14.545 0.601 19.922 1.315 2.841 -2.877 OAI 1YD 26 1YD OAE OAE O 0 1 N N N 13.998 -1.486 18.639 0.788 3.158 -0.429 OAE 1YD 27 1YD "O5'" O5* O 0 1 N N N 16.242 -0.603 18.493 -0.781 1.704 -1.770 "O5'" 1YD 28 1YD "C5'" C5* C 0 1 N N N 17.118 -1.707 18.313 -1.893 2.307 -1.107 "C5'" 1YD 29 1YD "C4'" C4* C 0 1 N N S 18.460 -1.054 18.288 -2.938 1.237 -0.786 "C4'" 1YD 30 1YD "O4'" O4* O 0 1 N N N 18.666 -0.627 16.968 -4.215 1.641 -1.284 "O4'" 1YD 31 1YD "C3'" C3* C 0 1 N N R 19.633 -1.940 18.378 -3.063 1.067 0.737 "C3'" 1YD 32 1YD "C2'" C2* C 0 1 N N R 20.660 -0.944 18.069 -4.578 1.058 1.014 "C2'" 1YD 33 1YD "O2'" O2* O 0 1 N N N 21.677 -1.665 17.400 -4.929 2.133 1.888 "O2'" 1YD 34 1YD "C1'" C1* C 0 1 N N R 19.908 -0.009 17.082 -5.235 1.251 -0.362 "C1'" 1YD 35 1YD N9 N9 N 0 1 Y N N 19.621 1.310 17.633 -5.845 -0.007 -0.799 N9 1YD 36 1YD C8 C8 C 0 1 Y N N 18.528 1.767 18.222 -5.271 -0.945 -1.605 C8 1YD 37 1YD N7 N7 N 0 1 Y N N 18.743 3.030 18.570 -6.093 -1.936 -1.789 N7 1YD 38 1YD C5 C5 C 0 1 Y N N 19.961 3.354 18.196 -7.244 -1.699 -1.115 C5 1YD 39 1YD C4 C4 C 0 1 Y N N 20.495 2.282 17.620 -7.096 -0.461 -0.467 C4 1YD 40 1YD N3 N3 N 0 1 Y N N 21.723 2.304 17.139 -8.097 0.003 0.275 N3 1YD 41 1YD C2 C2 C 0 1 Y N N 22.468 3.447 17.225 -9.211 -0.686 0.406 C2 1YD 42 1YD N1 N1 N 0 1 Y N N 21.905 4.546 17.834 -9.394 -1.855 -0.181 N1 1YD 43 1YD C6 C6 C 0 1 Y N N 20.667 4.464 18.303 -8.454 -2.395 -0.949 C6 1YD 44 1YD N6 N6 N 0 1 N N N 20.104 5.502 18.886 -8.655 -3.621 -1.558 N6 1YD 45 1YD H1 H1 H 0 1 N N N 15.686 5.518 25.149 10.366 -0.747 -0.550 H1 1YD 46 1YD H2 H2 H 0 1 N N N 12.962 3.488 25.927 10.472 1.207 0.730 H2 1YD 47 1YD H3 H3 H 0 1 N N N 13.638 5.083 25.936 9.078 1.853 1.411 H3 1YD 48 1YD H4 H4 H 0 1 N N N 18.361 0.114 22.962 4.233 -2.776 -0.792 H4 1YD 49 1YD H5 H5 H 0 1 N N N 15.057 -0.414 24.832 4.760 0.028 1.706 H5 1YD 50 1YD H6 H6 H 0 1 N N N 14.735 0.270 22.059 4.081 0.553 -1.161 H6 1YD 51 1YD H7 H7 H 0 1 N N N 13.045 -0.510 23.525 5.385 2.032 0.222 H7 1YD 52 1YD H8 H8 H 0 1 N N N 17.179 -0.619 22.292 1.430 -1.199 0.070 H8 1YD 53 1YD H9 H9 H 0 1 N N N 17.474 -3.267 21.384 1.719 -0.794 2.888 H9 1YD 54 1YD H10 H10 H 0 1 N N N 18.128 -3.246 23.057 1.064 0.714 2.206 H10 1YD 55 1YD H11 H11 H 0 1 N N N 21.579 -3.223 22.211 -0.526 1.202 3.710 H11 1YD 56 1YD H12 H12 H 0 1 N N N 14.993 -2.733 22.272 2.045 1.590 0.769 H12 1YD 57 1YD H13 H13 H 0 1 N N N 13.644 0.743 19.656 0.821 3.619 -3.171 H13 1YD 58 1YD H14 H14 H 0 1 N N N 16.912 -2.228 17.366 -1.555 2.774 -0.182 H14 1YD 59 1YD H15 H15 H 0 1 N N N 17.038 -2.418 19.148 -2.336 3.064 -1.755 H15 1YD 60 1YD H16 H16 H 0 1 N N N 18.517 -0.231 19.015 -2.648 0.289 -1.240 H16 1YD 61 1YD H17 H17 H 0 1 N N N 19.588 -2.675 17.561 -2.589 1.902 1.252 H17 1YD 62 1YD H18 H18 H 0 1 N N N 21.011 -0.398 18.957 -4.878 0.105 1.448 H18 1YD 63 1YD H19 H19 H 0 1 N N N 22.125 -2.230 18.019 -5.872 2.177 2.098 H19 1YD 64 1YD H20 H20 H 0 1 N N N 20.446 0.054 16.125 -5.996 2.029 -0.302 H20 1YD 65 1YD H21 H21 H 0 1 N N N 17.619 1.209 18.390 -4.280 -0.875 -2.028 H21 1YD 66 1YD H22 H22 H 0 1 N N N 23.471 3.487 16.826 -10.004 -0.281 1.016 H22 1YD 67 1YD H23 H23 H 0 1 N N N 20.745 6.270 18.892 -7.956 -4.010 -2.107 H23 1YD 68 1YD H24 H24 H 0 1 N N N 19.280 5.761 18.382 -9.494 -4.092 -1.436 H24 1YD 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 1YD "O4'" "C1'" SING N N 1 1YD "O4'" "C4'" SING N N 2 1YD "C1'" N9 SING N N 3 1YD "C1'" "C2'" SING N N 4 1YD N3 C2 DOUB Y N 5 1YD N3 C4 SING Y N 6 1YD C2 N1 SING Y N 7 1YD "O2'" "C2'" SING N N 8 1YD C4 N9 SING Y N 9 1YD C4 C5 DOUB Y N 10 1YD N9 C8 SING Y N 11 1YD N1 C6 DOUB Y N 12 1YD "C2'" "C3'" SING N N 13 1YD C5 C6 SING Y N 14 1YD C5 N7 SING Y N 15 1YD C8 N7 DOUB Y N 16 1YD "C4'" "C5'" SING N N 17 1YD "C4'" "C3'" SING N N 18 1YD C6 N6 SING N N 19 1YD "C5'" "O5'" SING N N 20 1YD "C3'" "O3'" SING N N 21 1YD "O5'" PBS SING N N 22 1YD OAE PBS DOUB N N 23 1YD PBS OAI SING N N 24 1YD PBS OAZ SING N N 25 1YD "O3'" PBR SING N N 26 1YD OAZ CBM SING N N 27 1YD PBR OAH DOUB N N 28 1YD PBR OAV SING N N 29 1YD PBR OAD SING N N 30 1YD OAV CAN SING N N 31 1YD CBM CBK SING N N 32 1YD CBM CBI SING N N 33 1YD CAN CBK SING N N 34 1YD CBK OAX SING N N 35 1YD CBI OAG SING N N 36 1YD CBI CBO SING N N 37 1YD CAL NAR DOUB Y N 38 1YD CAL NBQ SING Y N 39 1YD NAR CBE SING Y N 40 1YD NBQ CBO SING N N 41 1YD NBQ CBG SING Y N 42 1YD OAX CBO SING N N 43 1YD CBE CBG DOUB Y N 44 1YD CBE CBC SING N N 45 1YD OAC CBC DOUB N N 46 1YD CBG NAS SING N N 47 1YD CBC NAT SING N N 48 1YD NAS CBA DOUB N N 49 1YD NAT CBA SING N N 50 1YD CBA NAA SING N N 51 1YD NAT H1 SING N N 52 1YD NAA H2 SING N N 53 1YD NAA H3 SING N N 54 1YD CAL H4 SING N N 55 1YD CBO H5 SING N N 56 1YD CBI H6 SING N N 57 1YD OAG H7 SING N N 58 1YD CBK H8 SING N N 59 1YD CAN H9 SING N N 60 1YD CAN H10 SING N N 61 1YD OAD H11 SING N N 62 1YD CBM H12 SING N N 63 1YD OAI H13 SING N N 64 1YD "C5'" H14 SING N N 65 1YD "C5'" H15 SING N N 66 1YD "C4'" H16 SING N N 67 1YD "C3'" H17 SING N N 68 1YD "C2'" H18 SING N N 69 1YD "O2'" H19 SING N N 70 1YD "C1'" H20 SING N N 71 1YD C8 H21 SING N N 72 1YD C2 H22 SING N N 73 1YD N6 H23 SING N N 74 1YD N6 H24 SING N N 75 # 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 1YD SMILES ACDLabs 12.01 "O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(O)OC4C(OC(n2c3ncnc(N)c3nc2)C4O)COP(=O)(OC5C6O)O)N" 1YD InChI InChI 1.03 ;InChI=1S/C20H24N10O13P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-10(31)12-6(40-18)1-38-45(36,37)43-13-7(2-39-44(34,35)42-12)41-19(11(13)32)30-5-26-9-16(30)27-20(22)28-17(9)33/h3-7,10-13,18-19,31-32H,1-2H2,(H,34,35)(H,36,37)(H2,21,23,24)(H3,22,27,28,33)/t6-,7-,10+,11+,12-,13-,18+,19+/m0/s1 ; 1YD InChIKey InChI 1.03 RFCBNSCSPXMEBK-OIFWLNRKSA-N 1YD SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H]4CO[P](O)(=O)O[C@@H]5[C@@H](O)[C@@H](O[C@H]5CO[P](O)(=O)O[C@@H]4[C@H]3O)n6cnc7c(N)ncnc67" 1YD SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67" 1YD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]4[C@@H](O3)COP(=O)(O[C@H]5[C@H](COP(=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N" 1YD SMILES "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)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 1YD "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-9-[(2R,3R,3aR,5S,7aS,9R,10R,10aR,12R,14aS)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 1YD "Create component" 2013-08-02 RCSB 1YD "Initial release" 2013-08-14 RCSB #