data_APC # _chem_comp.id APC _chem_comp.name "DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H18 N5 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2021-03-13 _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 505.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code APC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1Q0N _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 APC PG PG P 0 1 N N N -6.128 1.979 4.000 1.239 -0.239 -7.092 PG APC 1 APC O1G O1G O 0 1 N N N -6.550 0.584 3.746 1.766 1.135 -6.944 O1G APC 2 APC O2G O2G O 0 1 N N N -4.954 2.409 3.152 2.173 -1.066 -8.109 O2G APC 3 APC O3G O3G O 0 1 N N N -5.869 2.260 5.475 -0.262 -0.179 -7.671 O3G APC 4 APC PB PB P 0 1 N N S -8.831 2.967 4.033 0.282 -0.093 -4.694 PB APC 5 APC O1B O1B O 0 1 N N N -8.809 2.248 5.381 0.824 1.279 -4.583 O1B APC 6 APC O2B O2B O 0 1 N N N -9.391 4.353 3.946 -1.202 -0.035 -5.314 O2B APC 7 APC O3B O3B O 0 1 N N N -7.305 2.979 3.537 1.231 -0.968 -5.656 O3B APC 8 APC PA PA P 0 1 N N R -11.427 1.800 3.170 -0.851 0.132 -1.952 PA APC 9 APC O1A O1A O 0 1 N N N -11.671 1.803 4.679 -0.309 1.505 -1.841 O1A APC 10 APC O2A O2A O 0 1 N N N -12.191 2.825 2.390 -2.336 0.190 -2.571 O2A APC 11 APC C3A C3A C 0 1 N N N -9.688 1.916 2.859 0.222 -0.858 -3.041 C3A APC 12 APC "O5'" O5* O 0 1 N N N -11.869 0.344 2.688 -0.905 -0.542 -0.491 "O5'" APC 13 APC "C5'" C5* C 0 1 N N N -11.915 0.041 1.228 -1.757 0.276 0.311 "C5'" APC 14 APC "C4'" C4* C 0 1 N N R -11.958 -1.459 1.125 -1.852 -0.313 1.720 "C4'" APC 15 APC "O4'" O4* O 0 1 N N N -10.751 -2.020 1.634 -0.549 -0.339 2.342 "O4'" APC 16 APC "C3'" C3* C 0 1 N N S -13.081 -2.180 1.774 -2.706 0.596 2.630 "C3'" APC 17 APC "O3'" O3* O 0 1 N N N -14.287 -2.101 1.131 -4.043 0.099 2.721 "O3'" APC 18 APC "C2'" C2* C 0 1 N N R -12.545 -3.556 1.941 -2.004 0.518 4.006 "C2'" APC 19 APC "O2'" O2* O 0 1 N N N -13.207 -4.507 1.074 -2.887 -0.026 4.989 "O2'" APC 20 APC "C1'" C1* C 0 1 N N R -11.059 -3.455 1.590 -0.807 -0.426 3.761 "C1'" APC 21 APC N9 N9 N 0 1 Y N N -10.119 -4.151 2.452 0.361 0.023 4.520 N9 APC 22 APC C8 C8 C 0 1 Y N N -9.101 -4.977 1.876 1.304 0.913 4.098 C8 APC 23 APC N7 N7 N 0 1 Y N N -8.347 -5.460 2.860 2.201 1.084 5.025 N7 APC 24 APC C5 C5 C 0 1 Y N N -8.893 -4.936 4.055 1.890 0.321 6.100 C5 APC 25 APC C6 C6 C 0 1 Y N N -8.462 -5.146 5.344 2.479 0.095 7.355 C6 APC 26 APC N6 N6 N 0 1 N N N -7.464 -5.866 5.767 3.646 0.745 7.717 N6 APC 27 APC N1 N1 N 0 1 Y N N -9.184 -4.506 6.347 1.887 -0.753 8.189 N1 APC 28 APC C2 C2 C 0 1 Y N N -10.187 -3.774 6.013 0.773 -1.378 7.852 C2 APC 29 APC N3 N3 N 0 1 Y N N -10.721 -3.485 4.735 0.189 -1.202 6.686 N3 APC 30 APC C4 C4 C 0 1 Y N N -9.970 -4.143 3.776 0.709 -0.373 5.787 C4 APC 31 APC HOG2 2HOG H 0 0 N N N -4.683 3.304 3.315 2.150 -0.597 -8.954 HOG2 APC 32 APC HOG3 3HOG H 0 0 N N N -5.598 3.155 5.638 -0.567 -1.093 -7.752 HOG3 APC 33 APC HOB2 2HOB H 0 0 N N N -9.404 4.800 3.107 -1.517 -0.948 -5.369 HOB2 APC 34 APC HOA2 2HOA H 0 0 N N N -12.039 2.823 1.452 -2.652 -0.721 -2.626 HOA2 APC 35 APC H3A1 1H3A H 0 0 N N N -9.492 2.247 1.812 1.227 -0.897 -2.622 H3A1 APC 36 APC H3A2 2H3A H 0 0 N N N -9.223 0.903 2.819 -0.176 -1.869 -3.123 H3A2 APC 37 APC "H5'1" 1H5* H 0 0 N N N -12.749 0.549 0.692 -2.751 0.312 -0.134 "H5'1" APC 38 APC "H5'2" 2H5* H 0 0 N N N -11.082 0.505 0.648 -1.347 1.284 0.366 "H5'2" APC 39 APC "H4'" H4* H 0 1 N N N -12.108 -1.608 0.030 -2.274 -1.317 1.682 "H4'" APC 40 APC "H3'" H3* H 0 1 N N N -13.369 -1.713 2.744 -2.705 1.620 2.256 "H3'" APC 41 APC "HO3'" *HO3 H 0 0 N N N -15.005 -2.562 1.546 -4.527 0.705 3.299 "HO3'" APC 42 APC "H2'" H2* H 0 1 N N N -12.713 -3.925 2.979 -1.654 1.504 4.312 "H2'" APC 43 APC "HO2'" *HO2 H 0 0 N N N -12.864 -5.386 1.180 -3.640 0.576 5.052 "HO2'" APC 44 APC "H1'" H1* H 0 1 N N N -10.926 -3.955 0.602 -1.067 -1.448 4.037 "H1'" APC 45 APC H8 H8 H 0 1 N N N -8.921 -5.210 0.813 1.306 1.404 3.136 H8 APC 46 APC HN61 1HN6 H 0 0 N N N -7.144 -6.021 6.723 4.041 0.584 8.588 HN61 APC 47 APC HN62 2HN6 H 0 0 N N N -6.648 -5.521 5.261 4.071 1.359 7.098 HN62 APC 48 APC H2 H2 H 0 1 N N N -10.639 -3.346 6.923 0.325 -2.060 8.560 H2 APC 49 # # 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 APC PG O1G DOUB N N 1 APC PG O2G SING N N 2 APC PG O3G SING N N 3 APC PG O3B SING N N 4 APC O2G HOG2 SING N N 5 APC O3G HOG3 SING N N 6 APC PB O1B DOUB N N 7 APC PB O2B SING N N 8 APC PB O3B SING N N 9 APC PB C3A SING N N 10 APC O2B HOB2 SING N N 11 APC PA O1A DOUB N N 12 APC PA O2A SING N N 13 APC PA C3A SING N N 14 APC PA "O5'" SING N N 15 APC O2A HOA2 SING N N 16 APC C3A H3A1 SING N N 17 APC C3A H3A2 SING N N 18 APC "O5'" "C5'" SING N N 19 APC "C5'" "C4'" SING N N 20 APC "C5'" "H5'1" SING N N 21 APC "C5'" "H5'2" SING N N 22 APC "C4'" "O4'" SING N N 23 APC "C4'" "C3'" SING N N 24 APC "C4'" "H4'" SING N N 25 APC "O4'" "C1'" SING N N 26 APC "C3'" "O3'" SING N N 27 APC "C3'" "C2'" SING N N 28 APC "C3'" "H3'" SING N N 29 APC "O3'" "HO3'" SING N N 30 APC "C2'" "O2'" SING N N 31 APC "C2'" "C1'" SING N N 32 APC "C2'" "H2'" SING N N 33 APC "O2'" "HO2'" SING N N 34 APC "C1'" N9 SING N N 35 APC "C1'" "H1'" SING N N 36 APC N9 C8 SING Y N 37 APC N9 C4 SING Y N 38 APC C8 N7 DOUB Y N 39 APC C8 H8 SING N N 40 APC N7 C5 SING Y N 41 APC C5 C6 SING Y N 42 APC C5 C4 DOUB Y N 43 APC C6 N6 SING N N 44 APC C6 N1 DOUB Y N 45 APC N6 HN61 SING N N 46 APC N6 HN62 SING N N 47 APC N1 C2 SING Y N 48 APC C2 N3 DOUB Y N 49 APC C2 H2 SING N N 50 APC N3 C4 SING Y N 51 # # 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 APC SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" APC SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" APC SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" APC 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)OP(=O)(O)O)O)O)O)N" APC SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N" APC InChI InChI 1.03 "InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1" APC InChIKey InChI 1.03 CAWZRIXWFRFUQB-IOSLPCCCSA-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 APC "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine" APC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methyl-phosphonooxy-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 APC "Create component" 1999-07-08 RCSB APC "Modify descriptor" 2011-06-04 RCSB APC "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id APC _pdbx_chem_comp_synonyms.name "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##