data_CGR # _chem_comp.id CGR _chem_comp.name "CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 N5 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "CYCLIC GDP-RIBOSE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-12-11 _chem_comp.pdbx_modified_date 2021-03-01 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 559.316 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CGR _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2O3T _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 CGR O2B O2B O 0 1 N N N 5.785 3.913 3.384 -2.291 -1.988 -0.495 O2B CGR 1 CGR PB PB P 0 1 N N S 4.366 4.424 3.562 -0.750 -2.414 -0.732 PB CGR 2 CGR O1B O1B O 0 1 N N N 3.914 5.789 3.098 -0.125 -1.889 -1.991 O1B CGR 3 CGR O3 O3 O 0 1 N N N 3.856 4.385 5.095 -0.778 -4.019 -0.602 O3 CGR 4 CGR PA PA P 0 1 N N S 4.416 3.356 6.218 -1.295 -5.197 -1.572 PA CGR 5 CGR O2A O2A O 0 1 N N N 5.852 3.707 6.565 -2.781 -5.253 -1.772 O2A CGR 6 CGR O1A O1A O 0 1 N N N 3.470 3.471 7.362 -0.440 -4.983 -2.929 O1A CGR 7 CGR "O5'R" RO5* O 0 0 N N N 3.394 3.408 2.784 -0.018 -1.973 0.641 "O5'R" CGR 8 CGR "C5'R" RC5* C 0 0 N N N 1.953 3.619 2.814 0.293 -0.605 0.864 "C5'R" CGR 9 CGR "C4'R" RC4* C 0 0 N N R 1.395 3.908 1.409 1.782 -0.447 1.149 "C4'R" CGR 10 CGR "O4'R" RO4* O 0 0 N N N 1.864 2.973 0.392 2.123 -1.129 2.368 "O4'R" CGR 11 CGR "C1'R" RC1* C 0 0 N N R 0.971 1.838 0.270 3.496 -1.581 2.285 "C1'R" CGR 12 CGR "C2'R" RC2* C 0 0 N N R -0.388 2.369 0.732 3.998 -1.217 0.886 "C2'R" CGR 13 CGR "O2'R" RO2* O 0 0 N N N -1.254 2.541 -0.418 4.739 0.001 0.950 "O2'R" CGR 14 CGR "C3'R" RC3* C 0 0 N N S -0.128 3.717 1.426 2.711 -1.040 0.103 "C3'R" CGR 15 CGR "O3'R" RO3* O 0 0 N N N -0.749 4.846 0.754 2.872 -0.207 -1.026 "O3'R" CGR 16 CGR N7 N7 N 0 1 N N N 1.528 0.773 1.173 3.617 -3.005 2.537 N7 CGR 17 CGR C8 C8 C 0 1 N N N 2.828 0.756 1.558 2.512 -3.945 2.299 C8 CGR 18 CGR N9 N9 N 0 1 N N N 3.060 -0.287 2.384 3.109 -5.231 2.706 N9 CGR 19 CGR "C1'" C1* C 0 1 N N R 4.329 -0.658 3.044 2.433 -6.509 2.552 "C1'" CGR 20 CGR "O4'" O4* O 0 1 N N N 4.084 -0.767 4.437 2.333 -6.883 1.160 "O4'" CGR 21 CGR "C2'" C2* C 0 1 N N R 5.376 0.427 2.872 1.011 -6.500 3.111 "C2'" CGR 22 CGR "O2'" O2* O 0 1 N N N 6.028 0.228 1.606 0.721 -7.789 3.654 "O2'" CGR 23 CGR "C3'" C3* C 0 1 N N S 6.237 0.223 4.100 0.171 -6.271 1.871 "C3'" CGR 24 CGR "O3'" O3* O 0 1 N N N 7.235 -0.785 3.801 -1.158 -6.731 2.006 "O3'" CGR 25 CGR "C4'" C4* C 0 1 N N R 5.259 -0.303 5.144 0.947 -7.046 0.817 "C4'" CGR 26 CGR "C5'" C5* C 0 1 N N N 4.803 0.741 6.152 0.732 -6.570 -0.612 "C5'" CGR 27 CGR "O5'" O5* O 0 1 N N N 4.318 1.926 5.496 -0.654 -6.537 -0.925 "O5'" CGR 28 CGR C4A C4A C 0 1 N N N 1.924 -0.958 2.550 4.458 -5.048 3.068 C4A CGR 29 CGR C5A C5A C 0 1 N N N 0.956 -0.312 1.804 4.723 -3.727 2.960 C5A CGR 30 CGR N3A N3A N 0 1 N N N 1.639 -2.055 3.280 5.384 -5.987 3.456 N3A CGR 31 CGR C2A C2A C 0 1 N N N 0.374 -2.543 3.256 6.587 -5.560 3.733 C2A CGR 32 CGR N2A N2A N 0 1 N N N 0.091 -3.633 3.982 7.590 -6.406 4.129 N2A CGR 33 CGR N1A N1A N 0 1 N N N -0.616 -1.956 2.517 6.937 -4.214 3.642 N1A CGR 34 CGR C6A C6A C 0 1 N N N -0.341 -0.839 1.770 6.066 -3.206 3.254 C6A CGR 35 CGR O6A O6A O 0 1 N N N -1.253 -0.329 1.084 6.370 -2.024 3.159 O6A CGR 36 CGR HO2B HO2B H 0 0 N N N 5.970 3.806 2.458 -2.700 -2.160 0.380 HO2B CGR 37 CGR HO1A HO1A H 0 0 N N N 3.959 3.495 8.176 -0.870 -5.167 -3.792 HO1A CGR 38 CGR H51 1H5 H 0 1 N N N 1.734 4.478 3.466 -0.295 -0.278 1.728 H51 CGR 39 CGR H52 2H5 H 0 1 N N N 1.477 2.703 3.193 0.002 -0.000 -0.001 H52 CGR 40 CGR "HC4'" HC4* H 0 0 N N N 1.725 4.929 1.166 1.993 0.620 1.294 "HC4'" CGR 41 CGR "HC1'" HC1* H 0 0 N N N 0.870 1.408 -0.737 4.036 -1.026 3.060 "HC1'" CGR 42 CGR "HC2'" HC2* H 0 0 N N N -0.882 1.672 1.425 4.659 -1.964 0.436 "HC2'" CGR 43 CGR HO2 HO2 H 0 1 N N N -2.159 2.579 -0.131 5.662 -0.234 1.153 HO2 CGR 44 CGR "HC3'" HC3* H 0 0 N N N -0.561 3.690 2.437 2.359 -2.020 -0.234 "HC3'" CGR 45 CGR HO3 HO3 H 0 1 N N N -0.885 5.550 1.377 3.204 0.641 -0.695 HO3 CGR 46 CGR H81 1H8 H 0 1 N N N 3.467 0.661 0.668 1.649 -3.697 2.924 H81 CGR 47 CGR H82 2H8 H 0 1 N N N 3.056 1.691 2.090 2.237 -3.962 1.240 H82 CGR 48 CGR "H1'" H1* H 0 1 N N N 4.690 -1.597 2.598 3.021 -7.295 3.042 "H1'" CGR 49 CGR "H2'" H2* H 0 1 N N N 5.026 1.469 2.825 0.831 -5.770 3.904 "H2'" CGR 50 CGR "HO2'" HO2* H 0 0 N N N 5.376 0.184 0.917 -0.068 -8.125 3.193 "HO2'" CGR 51 CGR "H3'" H3* H 0 1 N N N 6.760 1.131 4.434 0.143 -5.205 1.628 "H3'" CGR 52 CGR "HO3'" HO3* H 0 0 N N N 7.453 -0.751 2.877 -1.571 -6.636 1.134 "HO3'" CGR 53 CGR "H4'" H4* H 0 1 N N N 5.779 -1.090 5.709 0.696 -8.113 0.875 "H4'" CGR 54 CGR "H5'1" 1H5* H 0 0 N N N 3.993 0.316 6.762 1.197 -5.589 -0.762 "H5'1" CGR 55 CGR "H5'2" 2H5* H 0 0 N N N 5.663 1.018 6.779 1.228 -7.251 -1.312 "H5'2" CGR 56 CGR H2A1 1H2A H 0 0 N N N -0.872 -3.880 3.872 7.387 -7.376 4.202 H2A1 CGR 57 CGR H2A2 2H2A H 0 0 N N N 0.747 -4.128 4.551 8.483 -6.017 4.329 H2A2 CGR 58 CGR HN1A HN1A H 0 0 N N N -1.539 -2.341 2.521 7.892 -3.955 3.870 HN1A CGR 59 # # 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 CGR O2B PB SING N N 1 CGR O2B HO2B SING N N 2 CGR PB "O5'R" SING N N 3 CGR PB O1B DOUB N N 4 CGR PB O3 SING N N 5 CGR O3 PA SING N N 6 CGR PA "O5'" SING N N 7 CGR PA O2A DOUB N N 8 CGR PA O1A SING N N 9 CGR O1A HO1A SING N N 10 CGR "O5'R" "C5'R" SING N N 11 CGR "C5'R" "C4'R" SING N N 12 CGR "C5'R" H51 SING N N 13 CGR "C5'R" H52 SING N N 14 CGR "C4'R" "O4'R" SING N N 15 CGR "C4'R" "C3'R" SING N N 16 CGR "C4'R" "HC4'" SING N N 17 CGR "O4'R" "C1'R" SING N N 18 CGR "C1'R" "C2'R" SING N N 19 CGR "C1'R" N7 SING N N 20 CGR "C1'R" "HC1'" SING N N 21 CGR "C2'R" "O2'R" SING N N 22 CGR "C2'R" "C3'R" SING N N 23 CGR "C2'R" "HC2'" SING N N 24 CGR "O2'R" HO2 SING N N 25 CGR "C3'R" "O3'R" SING N N 26 CGR "C3'R" "HC3'" SING N N 27 CGR "O3'R" HO3 SING N N 28 CGR N7 C8 SING N N 29 CGR N7 C5A SING N N 30 CGR C8 N9 SING N N 31 CGR C8 H81 SING N N 32 CGR C8 H82 SING N N 33 CGR N9 C4A SING N N 34 CGR N9 "C1'" SING N N 35 CGR "C1'" "C2'" SING N N 36 CGR "C1'" "O4'" SING N N 37 CGR "C1'" "H1'" SING N N 38 CGR "O4'" "C4'" SING N N 39 CGR "C2'" "O2'" SING N N 40 CGR "C2'" "C3'" SING N N 41 CGR "C2'" "H2'" SING N N 42 CGR "O2'" "HO2'" SING N N 43 CGR "C3'" "O3'" SING N N 44 CGR "C3'" "C4'" SING N N 45 CGR "C3'" "H3'" SING N N 46 CGR "O3'" "HO3'" SING N N 47 CGR "C4'" "C5'" SING N N 48 CGR "C4'" "H4'" SING N N 49 CGR "C5'" "O5'" SING N N 50 CGR "C5'" "H5'1" SING N N 51 CGR "C5'" "H5'2" SING N N 52 CGR C4A C5A DOUB N N 53 CGR C4A N3A SING N N 54 CGR C5A C6A SING N N 55 CGR N3A C2A DOUB N N 56 CGR C2A N1A SING N N 57 CGR C2A N2A SING N N 58 CGR N2A H2A1 SING N N 59 CGR N2A H2A2 SING N N 60 CGR N1A C6A SING N N 61 CGR N1A HN1A SING N N 62 CGR C6A O6A DOUB N N 63 # # 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 CGR SMILES ACDLabs 10.04 "O=C1C=2N3CN(C=2N=C(N)N1)C5OC(COP(=O)(O)OP(=O)(O)OCC4OC3C(O)C4O)C(O)C5O" CGR SMILES_CANONICAL CACTVS 3.341 "NC1=NC2=C(N3CN2[C@@H]4O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]5O[C@@H]3[C@H](O)[C@@H]5O)[C@@H](O)[C@H]4O)C(=O)N1" CGR SMILES CACTVS 3.341 "NC1=NC2=C(N3CN2[CH]4O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]5O[CH]3[CH](O)[CH]5O)[CH](O)[CH]4O)C(=O)N1" CGR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]2[C@H]([C@H]([C@@H](O2)N3CN([C@H]4[C@@H]([C@@H]([C@H](O4)CO[P@@](=O)(O[P@](=O)(O1)O)O)O)O)C5=C3C(=O)NC(=N5)N)O)O" CGR SMILES "OpenEye OEToolkits" 1.5.0 "C1C2C(C(C(O2)N3CN(C4C(C(C(O4)COP(=O)(OP(=O)(O1)O)O)O)O)C5=C3C(=O)NC(=N5)N)O)O" CGR InChI InChI 1.03 "InChI=1S/C15H23N5O14P2/c16-15-17-11-6(12(25)18-15)19-3-20(11)14-10(24)8(22)5(33-14)2-31-36(28,29)34-35(26,27)30-1-4-7(21)9(23)13(19)32-4/h4-5,7-10,13-14,21-24H,1-3H2,(H,26,27)(H,28,29)(H3,16,17,18,25)/t4-,5-,7-,8-,9-,10-,13-,14-/m1/s1" CGR InChIKey InChI 1.03 XBIQPWWXYHHVOT-AIKIOGRUSA-N # _pdbx_chem_comp_identifier.comp_id CGR _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 10.04 _pdbx_chem_comp_identifier.identifier "(2R,3R,4S,5R,8S,10S,13R,14S,15R,16R)-20-amino-3,4,8,10,14,15-hexahydroxy-7,9,11,25,26-pentaoxa-1,17,19,21-tetraaza-8,10-diphosphapentacyclo[15.6.1.1~2,5~.1~13,16~.0~18,23~]hexacosa-18(23),19-dien-22-one 8,10-dioxide (non-preferred name)" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CGR "Create component" 2006-12-11 RCSB CGR "Modify descriptor" 2011-06-04 RCSB CGR "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CGR _pdbx_chem_comp_synonyms.name "CYCLIC GDP-RIBOSE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##