data_C2E # _chem_comp.id C2E _chem_comp.name "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H24 N10 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "c-di-GMP; Cyclic diguanosine monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-10-15 _chem_comp.pdbx_modified_date 2020-01-26 _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 690.411 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C2E _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 2RDE _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 C2E P1 P1 P 0 1 N N N 2.904 -21.000 -7.328 0.818 2.310 0.549 P1 C2E 1 C2E O2P O2P O 0 1 N N N 2.614 -20.463 -5.950 1.042 2.707 -0.994 O2P C2E 2 C2E O1P O1P O 0 1 N N N 2.870 -22.498 -7.405 0.594 3.536 1.347 O1P C2E 3 C2E "O5'" "O5'" O 0 1 N N N 1.861 -20.471 -8.398 -0.465 1.347 0.674 "O5'" C2E 4 C2E "C5'" "C5'" C 0 1 N N N 1.971 -20.901 -9.750 -1.805 1.794 0.465 "C5'" C2E 5 C2E "C4'" "C4'" C 0 1 N N R 0.899 -20.225 -10.577 -2.785 0.799 1.090 "C4'" C2E 6 C2E "O4'" "O4'" O 0 1 N N N -0.389 -20.452 -9.994 -4.110 1.332 1.035 "O4'" C2E 7 C2E "C3'" "C3'" C 0 1 N N S 1.063 -18.717 -10.636 -2.778 -0.516 0.295 "C3'" C2E 8 C2E "O3'" "O3'" O 0 1 N N N 2.000 -18.334 -11.654 -2.127 -1.548 1.040 "O3'" C2E 9 C2E "C2'" "C2'" C 0 1 N N R -0.350 -18.292 -10.868 -4.264 -0.862 0.085 "C2'" C2E 10 C2E "O2'" "O2'" O 0 1 N N N -0.626 -18.346 -12.271 -4.576 -2.109 0.709 "O2'" C2E 11 C2E "C1'" "C1'" C 0 1 N N R -1.212 -19.291 -10.119 -5.039 0.281 0.760 "C1'" C2E 12 C2E N9 N9 N 0 1 Y N N -1.507 -18.784 -8.781 -6.089 0.768 -0.139 N9 C2E 13 C2E C8 C8 C 0 1 Y N N -1.074 -19.304 -7.629 -5.990 1.824 -0.998 C8 C2E 14 C2E N7 N7 N 0 1 Y N N -1.523 -18.591 -6.578 -7.110 1.975 -1.641 N7 C2E 15 C2E C5 C5 C 0 1 Y N N -2.263 -17.593 -7.067 -7.992 1.029 -1.236 C5 C2E 16 C2E C6 C6 C 0 1 N N N -3.030 -16.469 -6.501 -9.327 0.715 -1.580 C6 C2E 17 C2E O6 O6 O 0 1 N N N -3.091 -16.295 -5.263 -9.927 1.369 -2.416 O6 C2E 18 C2E N1 N1 N 0 1 N N N -3.665 -15.645 -7.344 -9.922 -0.328 -0.959 N1 C2E 19 C2E C2 C2 C 0 1 N N N -3.615 -15.816 -8.681 -9.241 -1.052 -0.026 C2 C2E 20 C2E N2 N2 N 0 1 N N N -4.278 -14.952 -9.485 -9.870 -2.106 0.588 N2 C2E 21 C2E N3 N3 N 0 1 N N N -2.924 -16.831 -9.266 -8.000 -0.771 0.302 N3 C2E 22 C2E C4 C4 C 0 1 Y N N -2.242 -17.727 -8.519 -7.345 0.244 -0.275 C4 C2E 23 C2E P11 P11 P 0 1 N N N 2.786 -17.024 -11.195 -0.797 -2.300 0.531 P11 C2E 24 C2E O21 O21 O 0 1 N N N 1.787 -15.967 -10.842 -0.918 -2.593 -1.048 O21 C2E 25 C2E O11 O11 O 0 1 N N N 3.645 -16.587 -12.339 -0.645 -3.580 1.259 O11 C2E 26 C2E O5A O5A O 0 1 N N N 3.695 -17.385 -9.945 0.488 -1.371 0.807 O5A C2E 27 C2E C5A C5A C 0 1 N N N 4.726 -18.365 -10.103 1.830 -1.807 0.588 C5A C2E 28 C2E C4A C4A C 0 1 N N R 5.447 -18.579 -8.792 2.809 -0.796 1.189 C4A C2E 29 C2E O4A O4A O 0 1 N N N 6.015 -17.354 -8.279 4.138 -1.319 1.133 O4A C2E 30 C2E C3A C3A C 0 1 N N S 4.537 -19.101 -7.690 2.785 0.505 0.373 C3A C2E 31 C2E O3A O3A O 0 1 N N N 4.390 -20.532 -7.761 2.122 1.542 1.101 O3A C2E 32 C2E C2A C2A C 0 1 N N R 5.239 -18.621 -6.460 4.267 0.869 0.161 C2A C2E 33 C2E O2A O2A O 0 1 N N N 6.209 -19.604 -6.062 4.568 2.114 0.795 O2A C2E 34 C2E C1A C1A C 0 1 N N R 5.915 -17.310 -6.851 5.057 -0.271 0.822 C1A C2E 35 C2E N91 N91 N 0 1 Y N N 5.066 -16.178 -6.432 6.081 -0.766 -0.102 N91 C2E 36 C2E C81 C81 C 0 1 Y N N 4.215 -15.478 -7.209 5.955 -1.826 -0.953 C81 C2E 37 C2E N71 N71 N 0 1 Y N N 3.584 -14.516 -6.498 7.057 -1.984 -1.625 N71 C2E 38 C2E C51 C51 C 0 1 Y N N 4.032 -14.594 -5.236 7.953 -1.039 -1.249 C51 C2E 39 C2E C61 C61 C 0 1 N N N 3.784 -13.882 -3.970 9.280 -0.731 -1.630 C61 C2E 40 C2E O61 O61 O 0 1 N N N 2.968 -12.941 -3.892 9.855 -1.391 -2.479 O61 C2E 41 C2E N11 N11 N 0 1 N N N 4.459 -14.276 -2.885 9.894 0.313 -1.031 N11 C2E 42 C2E C21 C21 C 0 1 N N N 5.352 -15.291 -2.919 9.241 1.044 -0.084 C21 C2E 43 C2E N21 N21 N 0 1 N N N 6.000 -15.627 -1.778 9.890 2.099 0.507 N21 C2E 44 C2E N31 N31 N 0 1 N N N 5.624 -15.989 -4.046 8.009 0.768 0.279 N31 C2E 45 C2E C41 C41 C 0 1 Y N N 5.008 -15.685 -5.212 7.335 -0.246 -0.275 C41 C2E 46 C2E HO2P HO2P H 0 0 N N N 2.456 -21.186 -5.355 0.295 3.174 -1.393 HO2P C2E 47 C2E "H5'1" "H5'1" H 0 0 N N N 2.963 -20.632 -10.142 -1.937 2.772 0.929 "H5'1" C2E 48 C2E "H5'2" "H5'2" H 0 0 N N N 1.842 -21.992 -9.801 -2.000 1.871 -0.604 "H5'2" C2E 49 C2E "H4'" "H4'" H 0 1 N N N 0.991 -20.653 -11.586 -2.507 0.607 2.125 "H4'" C2E 50 C2E "H3'" "H3'" H 0 1 N N N 1.496 -18.240 -9.745 -2.284 -0.379 -0.669 "H3'" C2E 51 C2E "H2'" "H2'" H 0 1 N N N -0.543 -17.266 -10.521 -4.497 -0.902 -0.979 "H2'" C2E 52 C2E "HO2'" "HO2'" H 0 0 N N N -1.523 -18.077 -12.428 -5.500 -2.378 0.609 "HO2'" C2E 53 C2E "H1'" "H1'" H 0 1 N N N -2.164 -19.486 -10.634 -5.484 -0.072 1.690 "H1'" C2E 54 C2E H8 H8 H 0 1 N N N -0.447 -20.180 -7.551 -5.113 2.442 -1.124 H8 C2E 55 C2E HN1 HN1 H 0 1 N N N -4.192 -14.881 -6.972 -10.837 -0.563 -1.179 HN1 C2E 56 C2E HN21 HN21 H 0 0 N N N -4.250 -15.071 -10.478 -10.786 -2.326 0.356 HN21 C2E 57 C2E HN22 HN22 H 0 0 N N N -4.796 -14.195 -9.086 -9.399 -2.631 1.254 HN22 C2E 58 C2E HO21 HO21 H 0 0 N N N 1.897 -15.221 -11.420 -0.151 -3.046 -1.424 HO21 C2E 59 C2E H511 H511 H 0 0 N N N 4.277 -19.315 -10.429 1.977 -2.778 1.060 H511 C2E 60 C2E H512 H512 H 0 0 N N N 5.445 -18.016 -10.859 2.013 -1.895 -0.483 H512 C2E 61 C2E H4A H4A H 0 1 N N N 6.226 -19.317 -9.034 2.539 -0.587 2.223 H4A C2E 62 C2E H3A H3A H 0 1 N N N 3.497 -18.746 -7.743 2.298 0.345 -0.591 H3A C2E 63 C2E H2A H2A H 0 1 N N N 4.554 -18.467 -5.613 4.496 0.921 -0.903 H2A C2E 64 C2E HO2A HO2A H 0 0 N N N 6.660 -19.306 -5.281 5.488 2.394 0.695 HO2A C2E 65 C2E H1A H1A H 0 1 N N N 6.899 -17.183 -6.377 5.530 0.089 1.736 H1A C2E 66 C2E H81 H81 H 0 1 N N N 4.058 -15.662 -8.262 5.073 -2.441 -1.052 H81 C2E 67 C2E HN11 HN11 H 0 0 N N N 4.298 -13.804 -2.018 10.804 0.543 -1.276 HN11 C2E 68 C2E HN24 HN24 H 0 0 N N N 6.662 -16.376 -1.781 10.800 2.315 0.250 HN24 C2E 69 C2E HN23 HN23 H 0 0 N N N 5.816 -15.126 -0.932 9.439 2.628 1.183 HN23 C2E 70 # 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 C2E P1 O2P SING N N 1 C2E O1P P1 DOUB N N 2 C2E "O5'" P1 SING N N 3 C2E "C5'" "O5'" SING N N 4 C2E "C4'" "O4'" SING N N 5 C2E "C4'" "C5'" SING N N 6 C2E "C3'" "C4'" SING N N 7 C2E "O3'" P11 SING N N 8 C2E "O3'" "C3'" SING N N 9 C2E "C2'" "C3'" SING N N 10 C2E "C2'" "C1'" SING N N 11 C2E "O2'" "C2'" SING N N 12 C2E "C1'" "O4'" SING N N 13 C2E "C1'" N9 SING N N 14 C2E N9 C4 SING Y N 15 C2E N9 C8 SING Y N 16 C2E C8 N7 DOUB Y N 17 C2E C5 N7 SING Y N 18 C2E C5 C6 SING N N 19 C2E C6 O6 DOUB N N 20 C2E N1 C6 SING N N 21 C2E C2 N1 SING N N 22 C2E N2 C2 SING N N 23 C2E N3 C2 DOUB N N 24 C2E N3 C4 SING N N 25 C2E C4 C5 DOUB Y N 26 C2E P11 O21 SING N N 27 C2E P11 O5A SING N N 28 C2E O11 P11 DOUB N N 29 C2E C5A O5A SING N N 30 C2E C5A C4A SING N N 31 C2E C4A O4A SING N N 32 C2E C4A C3A SING N N 33 C2E O4A C1A SING N N 34 C2E C3A C2A SING N N 35 C2E O3A C3A SING N N 36 C2E O3A P1 SING N N 37 C2E C2A O2A SING N N 38 C2E C1A C2A SING N N 39 C2E C1A N91 SING N N 40 C2E N91 C41 SING Y N 41 C2E C81 N71 DOUB Y N 42 C2E C81 N91 SING Y N 43 C2E N71 C51 SING Y N 44 C2E C51 C41 DOUB Y N 45 C2E C51 C61 SING N N 46 C2E C61 O61 DOUB N N 47 C2E C61 N11 SING N N 48 C2E C21 N11 SING N N 49 C2E C21 N21 SING N N 50 C2E N31 C21 DOUB N N 51 C2E C41 N31 SING N N 52 C2E O2P HO2P SING N N 53 C2E "C5'" "H5'1" SING N N 54 C2E "C5'" "H5'2" SING N N 55 C2E "C4'" "H4'" SING N N 56 C2E "C3'" "H3'" SING N N 57 C2E "C2'" "H2'" SING N N 58 C2E "O2'" "HO2'" SING N N 59 C2E "C1'" "H1'" SING N N 60 C2E C8 H8 SING N N 61 C2E N1 HN1 SING N N 62 C2E N2 HN21 SING N N 63 C2E N2 HN22 SING N N 64 C2E O21 HO21 SING N N 65 C2E C5A H511 SING N N 66 C2E C5A H512 SING N N 67 C2E C4A H4A SING N N 68 C2E C3A H3A SING N N 69 C2E C2A H2A SING N N 70 C2E O2A HO2A SING N N 71 C2E C1A H1A SING N N 72 C2E C81 H81 SING N N 73 C2E N11 HN11 SING N N 74 C2E N21 HN24 SING N N 75 C2E N21 HN23 SING N N 76 # 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 C2E SMILES ACDLabs 11.02 "O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(OC4C(OC(n2c3N=C(N)NC(=O)c3nc2)C4O)COP(=O)(O)OC5C6O)O)N" C2E SMILES_CANONICAL CACTVS 3.352 "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(=O)NC(=Nc67)N" C2E SMILES CACTVS 3.352 "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(=O)NC(=Nc67)N" C2E SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N" C2E SMILES "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N" C2E InChI InChI 1.03 "InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1" C2E InChIKey InChI 1.03 PKFDLKSEZWEFGL-MHARETSRSA-N # _pdbx_chem_comp_identifier.comp_id C2E _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 11.02 _pdbx_chem_comp_identifier.identifier "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-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 C2E "Create component" 2007-10-15 EBI C2E "Modify aromatic_flag" 2011-06-04 RCSB C2E "Modify descriptor" 2011-06-04 RCSB C2E "Modify synonyms" 2019-12-17 PDBE C2E "Modify synonyms" 2020-01-26 RCSB # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 C2E "Cyclic diguanosine monophosphate" ? ? 2 C2E c-di-GMP ? ? #