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 
# 
