data_7D3 # _chem_comp.id 7D3 _chem_comp.name "[(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl trihydrogen diphosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O9 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "oxetanocin A diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-10-07 _chem_comp.pdbx_modified_date 2020-06-17 _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 411.202 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 7D3 _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 5TK6 _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 7D3 C01 C1 C 0 1 Y N N -8.271 -16.932 -15.636 6.685 1.121 0.462 C01 7D3 1 7D3 N02 N1 N 0 1 Y N N -7.459 -17.509 -16.525 5.386 1.076 0.675 N02 7D3 2 7D3 C03 C2 C 0 1 Y N N -6.553 -18.482 -16.141 4.697 -0.032 0.423 C03 7D3 3 7D3 C04 C3 C 0 1 Y N N -6.496 -18.853 -14.789 5.373 -1.158 -0.076 C04 7D3 4 7D3 C05 C4 C 0 1 Y N N -7.379 -18.203 -13.877 6.759 -1.061 -0.287 C05 7D3 5 7D3 N06 N2 N 0 1 Y N N -8.245 -17.256 -14.341 7.363 0.089 -0.005 N06 7D3 6 7D3 N07 N3 N 0 1 N N N -7.363 -18.542 -12.522 7.478 -2.137 -0.776 N07 7D3 7 7D3 N08 N4 N 0 1 Y N N -5.532 -19.816 -14.684 4.450 -2.136 -0.244 N08 7D3 8 7D3 C09 C5 C 0 1 Y N N -5.016 -20.030 -15.904 3.279 -1.692 0.112 C09 7D3 9 7D3 N10 N5 N 0 1 Y N N -5.597 -19.229 -16.807 3.379 -0.398 0.531 N10 7D3 10 7D3 C11 C6 C 0 1 N N R -5.349 -19.205 -18.188 2.281 0.445 1.009 C11 7D3 11 7D3 C12 C7 C 0 1 N N R -3.975 -19.044 -18.722 1.625 1.298 -0.093 C12 7D3 12 7D3 C13 C8 C 0 1 N N S -3.974 -20.386 -19.112 0.284 0.888 0.545 C13 7D3 13 7D3 O14 O1 O 0 1 N N N -5.382 -20.510 -18.709 1.013 -0.236 1.085 O14 7D3 14 7D3 C15 C9 C 0 1 N N N -3.019 -21.223 -18.300 -0.792 0.501 -0.471 C15 7D3 15 7D3 O16 O2 O 0 1 N N N -3.676 -22.360 -17.870 -2.023 0.252 0.211 O16 7D3 16 7D3 P17 P1 P 0 1 N N N -2.996 -23.377 -16.866 -3.375 -0.181 -0.550 P17 7D3 17 7D3 O18 O3 O 0 1 N N N -2.541 -22.781 -15.589 -3.171 -1.628 -1.225 O18 7D3 18 7D3 O19 O4 O 0 1 N N N -1.814 -23.978 -17.551 -3.690 0.814 -1.599 O19 7D3 19 7D3 O20 O5 O 0 1 N N N -4.082 -24.526 -16.489 -4.588 -0.248 0.507 O20 7D3 20 7D3 P21 P2 P 0 1 N N N -4.246 -25.877 -17.335 -6.190 -0.308 0.368 P21 7D3 21 7D3 O22 O6 O 0 1 N N N -4.628 -25.487 -18.748 -6.625 0.593 -0.723 O22 7D3 22 7D3 O23 O7 O 0 1 N N N -2.914 -26.651 -17.372 -6.643 -1.816 0.032 O23 7D3 23 7D3 O24 O8 O 0 1 N N N -5.396 -26.794 -16.627 -6.867 0.160 1.752 O24 7D3 24 7D3 C29 C10 C 0 1 N N N -3.875 -18.051 -19.942 1.933 2.793 0.016 C29 7D3 25 7D3 O30 O9 O 0 1 N N N -4.313 -18.585 -21.166 1.380 3.477 -1.110 O30 7D3 26 7D3 H1 H1 H 0 1 N N N -8.969 -16.181 -15.974 7.214 2.038 0.674 H1 7D3 27 7D3 H2 H2 H 0 1 N N N -8.046 -17.999 -12.034 7.025 -2.971 -0.978 H2 7D3 28 7D3 H3 H3 H 0 1 N N N -7.575 -19.514 -12.419 8.434 -2.058 -0.917 H3 7D3 29 7D3 H4 H4 H 0 1 N N N -4.240 -20.748 -16.127 2.364 -2.264 0.080 H4 7D3 30 7D3 H5 H5 H 0 1 N N N -6.048 -18.539 -18.716 2.535 1.006 1.908 H5 7D3 31 7D3 H6 H6 H 0 1 N N N -3.239 -18.798 -17.942 1.771 0.905 -1.099 H6 7D3 32 7D3 H7 H7 H 0 1 N N N -3.831 -20.533 -20.193 -0.074 1.584 1.304 H7 7D3 33 7D3 H8 H8 H 0 1 N N N -2.157 -21.507 -18.921 -0.929 1.314 -1.183 H8 7D3 34 7D3 H9 H9 H 0 1 N N N -2.670 -20.647 -17.430 -0.483 -0.399 -1.003 H9 7D3 35 7D3 H10 H10 H 0 1 N N N -1.605 -22.914 -15.493 -2.961 -2.330 -0.595 H10 7D3 36 7D3 H11 H11 H 0 1 N N N -2.613 -26.721 -18.270 -6.391 -2.462 0.706 H11 7D3 37 7D3 H12 H12 H 0 1 N N N -6.115 -26.925 -17.234 -7.834 0.148 1.741 H12 7D3 38 7D3 H13 H13 H 0 1 N N N -2.823 -17.751 -20.055 1.495 3.188 0.933 H13 7D3 39 7D3 H14 H14 H 0 1 N N N -4.487 -17.165 -19.715 3.013 2.940 0.036 H14 7D3 40 7D3 H15 H15 H 0 1 N N N -4.222 -17.930 -21.848 1.537 4.431 -1.106 H15 7D3 41 # # 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 7D3 O30 C29 SING N N 1 7D3 C29 C12 SING N N 2 7D3 C13 C12 SING N N 3 7D3 C13 O14 SING N N 4 7D3 C13 C15 SING N N 5 7D3 O22 P21 DOUB N N 6 7D3 C12 C11 SING N N 7 7D3 O14 C11 SING N N 8 7D3 C15 O16 SING N N 9 7D3 C11 N10 SING N N 10 7D3 O16 P17 SING N N 11 7D3 O19 P17 DOUB N N 12 7D3 O23 P21 SING N N 13 7D3 P21 O24 SING N N 14 7D3 P21 O20 SING N N 15 7D3 P17 O20 SING N N 16 7D3 P17 O18 SING N N 17 7D3 N10 C03 SING Y N 18 7D3 N10 C09 SING Y N 19 7D3 N02 C03 DOUB Y N 20 7D3 N02 C01 SING Y N 21 7D3 C03 C04 SING Y N 22 7D3 C09 N08 DOUB Y N 23 7D3 C01 N06 DOUB Y N 24 7D3 C04 N08 SING Y N 25 7D3 C04 C05 DOUB Y N 26 7D3 N06 C05 SING Y N 27 7D3 C05 N07 SING N N 28 7D3 C01 H1 SING N N 29 7D3 N07 H2 SING N N 30 7D3 N07 H3 SING N N 31 7D3 C09 H4 SING N N 32 7D3 C11 H5 SING N N 33 7D3 C12 H6 SING N N 34 7D3 C13 H7 SING N N 35 7D3 C15 H8 SING N N 36 7D3 C15 H9 SING N N 37 7D3 O18 H10 SING N N 38 7D3 O23 H11 SING N N 39 7D3 O24 H12 SING N N 40 7D3 C29 H13 SING N N 41 7D3 C29 H14 SING N N 42 7D3 O30 H15 SING N N 43 # # 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 7D3 SMILES ACDLabs 12.01 "c1nc(c2c(n1)n(cn2)C3C(C(O3)COP(OP(O)(=O)O)(O)=O)CO)N" 7D3 InChI InChI 1.03 "InChI=1S/C10H15N5O9P2/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(23-10)2-22-26(20,21)24-25(17,18)19/h3-6,10,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6-,10-/m1/s1" 7D3 InChIKey InChI 1.03 HJOFGDMHIXEUNX-OXOINMOOSA-N 7D3 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@H]3CO" 7D3 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH]3CO" 7D3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)CO)N" 7D3 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(O3)COP(=O)(O)OP(=O)(O)O)CO)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 7D3 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl trihydrogen diphosphate" 7D3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{S},3~{R},4~{R})-4-(6-aminopurin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl phosphono 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 7D3 "Create component" 2016-10-07 RCSB 7D3 "Initial release" 2016-11-23 RCSB 7D3 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 7D3 _pdbx_chem_comp_synonyms.name "oxetanocin A diphosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##