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                           ? ? 
# 
