data_A12 # _chem_comp.id A12 _chem_comp.name "PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N5 O9 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-12-15 _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 425.228 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A12 _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 1HPU _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 A12 PB PB P 0 1 N N N -2.904 -0.420 -1.838 -6.106 1.026 -0.312 PB A12 1 A12 O1B O1B O 0 1 N N N -1.601 -0.830 -2.460 -6.748 -0.266 0.019 O1B A12 2 A12 O2B O2B O 0 1 N N N -2.880 -0.654 -0.363 -5.912 1.889 1.033 O2B A12 3 A12 O3B O3B O 0 1 N N N -3.172 1.022 -2.074 -7.039 1.840 -1.341 O3B A12 4 A12 PA PA P 0 1 N N S -5.850 -0.876 -1.948 -3.425 -0.203 0.087 PA A12 5 A12 O1A O1A O 0 1 N N N -5.873 -0.862 -0.461 -4.066 -1.495 0.418 O1A A12 6 A12 O2A O2A O 0 1 N N N -6.860 -1.819 -2.490 -3.230 0.659 1.433 O2A A12 7 A12 C3A C3A C 0 1 N N N -4.236 -1.356 -2.511 -4.481 0.719 -1.078 C3A A12 8 A12 "O5'" O5* O 0 1 N N N -6.160 0.599 -2.462 -1.989 -0.474 -0.589 "O5'" A12 9 A12 "C5'" C5* C 0 1 N N N -6.136 0.837 -3.854 -1.253 -1.297 0.319 "C5'" A12 10 A12 "C4'" C4* C 0 1 N N R -7.018 2.009 -4.197 0.129 -1.593 -0.267 "C4'" A12 11 A12 "O4'" O4* O 0 1 N N N -6.428 3.242 -3.692 0.912 -0.383 -0.344 "O4'" A12 12 A12 "C3'" C3* C 0 1 N N S -7.147 2.222 -5.693 0.927 -2.521 0.676 "C3'" A12 13 A12 "O3'" O3* O 0 1 N N N -8.203 1.386 -6.173 0.844 -3.877 0.233 "O3'" A12 14 A12 "C2'" C2* C 0 1 N N R -7.457 3.712 -5.783 2.381 -2.004 0.570 "C2'" A12 15 A12 "O2'" O2* O 0 1 N N N -8.798 3.978 -5.471 3.240 -3.026 0.061 "O2'" A12 16 A12 "C1'" C1* C 0 1 N N R -6.582 4.277 -4.653 2.286 -0.823 -0.421 "C1'" A12 17 A12 N9 N9 N 0 1 Y N N -5.252 4.698 -5.096 3.191 0.256 -0.018 N9 A12 18 A12 C8 C8 C 0 1 Y N N -4.069 4.025 -4.919 2.870 1.330 0.758 C8 A12 19 A12 N7 N7 N 0 1 Y N N -3.024 4.642 -5.428 3.913 2.091 0.918 N7 A12 20 A12 C5 C5 C 0 1 Y N N -3.557 5.801 -5.970 4.969 1.552 0.262 C5 A12 21 A12 C6 C6 C 0 1 Y N N -2.965 6.882 -6.634 6.312 1.923 0.077 C6 A12 22 A12 N6 N6 N 0 1 N N N -1.655 6.979 -6.857 6.813 3.078 0.651 N6 A12 23 A12 N1 N1 N 0 1 Y N N -3.771 7.877 -7.062 7.091 1.135 -0.658 N1 A12 24 A12 C2 C2 C 0 1 Y N N -5.082 7.790 -6.807 6.621 0.031 -1.210 C2 A12 25 A12 N3 N3 N 0 1 Y N N -5.760 6.828 -6.174 5.370 -0.352 -1.069 N3 A12 26 A12 C4 C4 C 0 1 Y N N -4.928 5.849 -5.778 4.516 0.371 -0.351 C4 A12 27 A12 HOB2 2HOB H 0 0 N N N -2.875 -1.588 -0.190 -5.492 2.720 0.774 HOB2 A12 28 A12 HXT HXT H 0 1 N N N -3.229 1.474 -1.241 -7.887 1.982 -0.898 HXT A12 29 A12 HOA2 2HOA H 0 0 N N N -7.499 -2.020 -1.817 -2.810 1.491 1.173 HOA2 A12 30 A12 H3A1 1H3A H 0 0 N N N -4.086 -2.393 -2.177 -4.008 1.670 -1.322 H3A1 A12 31 A12 H3A2 2H3A H 0 0 N N N -4.213 -1.232 -3.604 -4.613 0.135 -1.989 H3A2 A12 32 A12 "H5'1" 1H5* H 0 0 N N N -6.506 -0.057 -4.378 -1.789 -2.232 0.477 "H5'1" A12 33 A12 "H5'2" 2H5* H 0 0 N N N -5.104 1.057 -4.166 -1.141 -0.777 1.270 "H5'2" A12 34 A12 "H4'" H4* H 0 1 N N N -7.998 1.783 -3.751 0.032 -2.047 -1.253 "H4'" A12 35 A12 "H3'" H3* H 0 1 N N N -6.267 1.963 -6.300 0.562 -2.431 1.699 "H3'" A12 36 A12 "HO3'" *HO3 H 0 0 N N N -8.808 1.201 -5.464 1.358 -4.407 0.857 "HO3'" A12 37 A12 "H2'" H2* H 0 1 N N N -7.276 4.126 -6.786 2.735 -1.657 1.541 "H2'" A12 38 A12 "HO2'" *HO2 H 0 0 N N N -8.898 4.038 -4.528 3.210 -3.757 0.693 "HO2'" A12 39 A12 "H1'" H1* H 0 1 N N N -7.078 5.173 -4.252 2.521 -1.157 -1.432 "H1'" A12 40 A12 H8 H8 H 0 1 N N N -4.002 3.076 -4.409 1.893 1.522 1.177 H8 A12 41 A12 HN61 1HN6 H 0 0 N N N -0.976 6.300 -6.577 7.743 3.321 0.519 HN61 A12 42 A12 HN62 2HN6 H 0 0 N N N -1.447 7.827 -7.345 6.233 3.646 1.182 HN62 A12 43 A12 H2 H2 H 0 1 N N N -5.678 8.617 -7.164 7.289 -0.579 -1.800 H2 A12 44 # # 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 A12 PB O1B DOUB N N 1 A12 PB O2B SING N N 2 A12 PB O3B SING N N 3 A12 PB C3A SING N N 4 A12 O2B HOB2 SING N N 5 A12 O3B HXT SING N N 6 A12 PA O1A DOUB N N 7 A12 PA O2A SING N N 8 A12 PA C3A SING N N 9 A12 PA "O5'" SING N N 10 A12 O2A HOA2 SING N N 11 A12 C3A H3A1 SING N N 12 A12 C3A H3A2 SING N N 13 A12 "O5'" "C5'" SING N N 14 A12 "C5'" "C4'" SING N N 15 A12 "C5'" "H5'1" SING N N 16 A12 "C5'" "H5'2" SING N N 17 A12 "C4'" "O4'" SING N N 18 A12 "C4'" "C3'" SING N N 19 A12 "C4'" "H4'" SING N N 20 A12 "O4'" "C1'" SING N N 21 A12 "C3'" "O3'" SING N N 22 A12 "C3'" "C2'" SING N N 23 A12 "C3'" "H3'" SING N N 24 A12 "O3'" "HO3'" SING N N 25 A12 "C2'" "O2'" SING N N 26 A12 "C2'" "C1'" SING N N 27 A12 "C2'" "H2'" SING N N 28 A12 "O2'" "HO2'" SING N N 29 A12 "C1'" N9 SING N N 30 A12 "C1'" "H1'" SING N N 31 A12 N9 C8 SING Y N 32 A12 N9 C4 SING Y N 33 A12 C8 N7 DOUB Y N 34 A12 C8 H8 SING N N 35 A12 N7 C5 SING Y N 36 A12 C5 C6 SING Y N 37 A12 C5 C4 DOUB Y N 38 A12 C6 N6 SING N N 39 A12 C6 N1 DOUB Y N 40 A12 N6 HN61 SING N N 41 A12 N6 HN62 SING N N 42 A12 N1 C2 SING Y N 43 A12 C2 N3 DOUB Y N 44 A12 C2 H2 SING N N 45 A12 N3 C4 SING Y N 46 # # 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 A12 SMILES ACDLabs 10.04 "O=P(O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" A12 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O" A12 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O" A12 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)(CP(=O)(O)O)O)O)O)N" A12 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N" A12 InChI InChI 1.03 "InChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1" A12 InChIKey InChI 1.03 OLCWZBFDIYXLAA-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 A12 "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine" A12 "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]methylphosphonic 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 A12 "Create component" 2000-12-15 RCSB A12 "Modify descriptor" 2011-06-04 RCSB A12 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A12 _pdbx_chem_comp_synonyms.name "ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##