data_A1AEP
# 
_chem_comp.id                                    A1AEP 
_chem_comp.name                                  "3'3'-cUMP-AMP" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H23 N7 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "1-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxooctahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-02-13 
_chem_comp.pdbx_modified_date                    2025-05-16 
_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                        635.372 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1AEP 
_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        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1AEP C13  C1  C 0 1 N N S N N N ? ? ? 3.128   -0.952 0.021  C13  A1AEP 1  
A1AEP C20  C2  C 0 1 N N N N N N ? ? ? 8.425   1.087  2.102  C20  A1AEP 2  
A1AEP C21  C3  C 0 1 N N N N N N ? ? ? 7.080   1.158  2.537  C21  A1AEP 3  
A1AEP C22  C4  C 0 1 N N N N N N ? ? ? 6.095   0.785  1.692  C22  A1AEP 4  
A1AEP C26  C5  C 0 1 N N R N N N ? ? ? 3.062   0.446  -0.613 C26  A1AEP 5  
A1AEP C02  C6  C 0 1 N N R N N N ? ? ? -3.673  1.135  0.136  C02  A1AEP 6  
A1AEP C03  C7  C 0 1 N N S N N N ? ? ? -2.226  0.758  -0.240 C03  A1AEP 7  
A1AEP C08  C8  C 0 1 N N R N N N ? ? ? -2.350  -0.516 -1.091 C08  A1AEP 8  
A1AEP C09  C9  C 0 1 N N N N N N ? ? ? -1.535  -1.644 -0.457 C09  A1AEP 9  
A1AEP C14  C10 C 0 1 N N R N N N ? ? ? 4.628   -1.299 0.068  C14  A1AEP 10 
A1AEP C16  C11 C 0 1 N N R N N N ? ? ? 5.342   -0.055 -0.483 C16  A1AEP 11 
A1AEP C18  C12 C 0 1 N N N N N N ? ? ? 7.693   0.286  0.032  C18  A1AEP 12 
A1AEP C27  C13 C 0 1 N N N N N N ? ? ? 2.115   1.338  0.193  C27  A1AEP 13 
A1AEP C32  C14 C 0 1 N N R N N N ? ? ? -4.547  0.203  -0.718 C32  A1AEP 14 
A1AEP C34  C15 C 0 1 Y N N N N N ? ? ? -6.863  0.323  0.296  C34  A1AEP 15 
A1AEP C36  C16 C 0 1 Y N N N N N ? ? ? -8.616  1.809  0.285  C36  A1AEP 16 
A1AEP C38  C17 C 0 1 Y N N N N N ? ? ? -8.901  -0.133 1.499  C38  A1AEP 17 
A1AEP C40  C18 C 0 1 Y N N N N N ? ? ? -7.609  -0.535 1.120  C40  A1AEP 18 
A1AEP C42  C19 C 0 1 Y N N N N N ? ? ? -5.696  -1.490 0.758  C42  A1AEP 19 
A1AEP N17  N1  N 0 1 N N N N N N ? ? ? 6.411   0.349  0.435  N17  A1AEP 20 
A1AEP N19  N2  N 0 1 N N N N N N ? ? ? 8.695   0.651  0.854  N19  A1AEP 21 
A1AEP N33  N3  N 0 1 Y N N N N N ? ? ? -5.661  -0.306 0.084  N33  A1AEP 22 
A1AEP N35  N4  N 0 1 Y N N N N N ? ? ? -7.402  1.473  -0.097 N35  A1AEP 23 
A1AEP N37  N5  N 0 1 Y N N N N N ? ? ? -9.353  1.038  1.064  N37  A1AEP 24 
A1AEP N39  N6  N 0 1 N N N N N N ? ? ? -9.681  -0.934 2.315  N39  A1AEP 25 
A1AEP N41  N7  N 0 1 Y N N N N N ? ? ? -6.839  -1.623 1.365  N41  A1AEP 26 
A1AEP O01  O1  O 0 1 N N N N N N ? ? ? -3.933  2.501  -0.191 O01  A1AEP 27 
A1AEP O04  O2  O 0 1 N N N N N N ? ? ? -1.618  1.806  -0.996 O04  A1AEP 28 
A1AEP O06  O3  O 0 1 N N N N N N ? ? ? 0.403   3.292  -1.277 O06  A1AEP 29 
A1AEP O07  O4  O 0 1 N N N N N N ? ? ? 0.264   1.246  -2.745 O07  A1AEP 30 
A1AEP O10  O5  O 0 1 N N N N N N ? ? ? -0.181  -1.554 -0.906 O10  A1AEP 31 
A1AEP O12  O6  O 0 1 N N N N N N ? ? ? 2.423   -1.898 -0.784 O12  A1AEP 32 
A1AEP O15  O7  O 0 1 N N N N N N ? ? ? 4.903   -2.435 -0.753 O15  A1AEP 33 
A1AEP O23  O8  O 0 1 N N N N N N ? ? ? 9.331   1.422  2.844  O23  A1AEP 34 
A1AEP O24  O9  O 0 1 N N N N N N ? ? ? 7.951   -0.105 -1.090 O24  A1AEP 35 
A1AEP O25  O10 O 0 1 N N N N N N ? ? ? 4.381   0.996  -0.595 O25  A1AEP 36 
A1AEP O28  O11 O 0 1 N N N N N N ? ? ? 0.763   1.053  -0.171 O28  A1AEP 37 
A1AEP O29  O12 O 0 1 N N N N N N ? ? ? 0.907   -2.634 1.098  O29  A1AEP 38 
A1AEP O30  O13 O 0 1 N N N N N N ? ? ? 0.830   -3.975 -1.038 O30  A1AEP 39 
A1AEP O31  O14 O 0 1 N N N N N N ? ? ? -3.729  -0.884 -1.155 O31  A1AEP 40 
A1AEP P05  P1  P 0 1 N N N N N N ? ? ? -0.038  1.880  -1.296 P05  A1AEP 41 
A1AEP P11  P2  P 0 1 N N N N N N ? ? ? 0.993   -2.517 -0.374 P11  A1AEP 42 
A1AEP H131 H1  H 0 0 N N N N N N ? ? ? 2.718   -0.929 1.031  H131 A1AEP 43 
A1AEP H211 H2  H 0 0 N N N N N N ? ? ? 6.845   1.504  3.533  H211 A1AEP 44 
A1AEP H221 H3  H 0 0 N N N N N N ? ? ? 5.063   0.832  2.008  H221 A1AEP 45 
A1AEP H261 H4  H 0 0 N N N N N N ? ? ? 2.710   0.368  -1.643 H261 A1AEP 46 
A1AEP H021 H5  H 0 0 N N N N N N ? ? ? -3.850  0.956  1.195  H021 A1AEP 47 
A1AEP H031 H6  H 0 0 N N N N N N ? ? ? -1.647  0.555  0.661  H031 A1AEP 48 
A1AEP H081 H7  H 0 0 N N N N N N ? ? ? -1.979  -0.320 -2.099 H081 A1AEP 49 
A1AEP H091 H8  H 0 0 N N N N N N ? ? ? -1.569  -1.551 0.628  H091 A1AEP 50 
A1AEP H092 H9  H 0 0 N N N N N N ? ? ? -1.954  -2.605 -0.753 H092 A1AEP 51 
A1AEP H141 H10 H 0 0 N N N N N N ? ? ? 4.941   -1.489 1.095  H141 A1AEP 52 
A1AEP H161 H11 H 0 0 N N N N N N ? ? ? 5.763   -0.276 -1.463 H161 A1AEP 53 
A1AEP H272 H12 H 0 0 N N N N N N ? ? ? 2.254   1.148  1.258  H272 A1AEP 54 
A1AEP H271 H13 H 0 0 N N N N N N ? ? ? 2.336   2.385  -0.018 H271 A1AEP 55 
A1AEP H321 H14 H 0 0 N N N N N N ? ? ? -4.931  0.746  -1.581 H321 A1AEP 56 
A1AEP H361 H15 H 0 0 N N N N N N ? ? ? -9.025  2.750  -0.052 H361 A1AEP 57 
A1AEP H421 H16 H 0 0 N N N N N N ? ? ? -4.893  -2.212 0.784  H421 A1AEP 58 
A1AEP H191 H17 H 0 0 N N N N N N ? ? ? 9.614   0.600  0.548  H191 A1AEP 59 
A1AEP H391 H18 H 0 0 N N N N N N ? ? ? -10.568 -0.642 2.576  H391 A1AEP 60 
A1AEP H392 H19 H 0 0 N N N N N N ? ? ? -9.340  -1.787 2.626  H392 A1AEP 61 
A1AEP H011 H20 H 0 0 N N N N N N ? ? ? -4.844  2.778  -0.025 H011 A1AEP 62 
A1AEP H1   H21 H 0 1 N N N N N N ? ? ? 1.198   1.257  -2.992 H1   A1AEP 63 
A1AEP H151 H22 H 0 0 N N N N N N ? ? ? 5.833   -2.699 -0.762 H151 A1AEP 64 
A1AEP H2   H23 H 0 1 N N N N N N ? ? ? -0.010  -4.409 -0.833 H2   A1AEP 65 
# 
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 
A1AEP C02 O01  SING N N 1  
A1AEP C03 C02  SING N N 2  
A1AEP P05 O04  SING N N 3  
A1AEP O06 P05  DOUB N N 4  
A1AEP O07 P05  SING N N 5  
A1AEP O04 C03  SING N N 6  
A1AEP C08 C03  SING N N 7  
A1AEP O10 C09  SING N N 8  
A1AEP P11 O10  SING N N 9  
A1AEP C13 O12  SING N N 10 
A1AEP C14 C13  SING N N 11 
A1AEP O15 C14  SING N N 12 
A1AEP C16 C14  SING N N 13 
A1AEP C18 N17  SING N N 14 
A1AEP C20 N19  SING N N 15 
A1AEP C22 C21  DOUB N N 16 
A1AEP C21 C20  SING N N 17 
A1AEP O23 C20  DOUB N N 18 
A1AEP N19 C18  SING N N 19 
A1AEP O24 C18  DOUB N N 20 
A1AEP N17 C16  SING N N 21 
A1AEP O25 C16  SING N N 22 
A1AEP C26 O25  SING N N 23 
A1AEP C27 C26  SING N N 24 
A1AEP O28 C27  SING N N 25 
A1AEP O12 P11  SING N N 26 
A1AEP O29 P11  DOUB N N 27 
A1AEP O30 P11  SING N N 28 
A1AEP C09 C08  SING N N 29 
A1AEP O31 C08  SING N N 30 
A1AEP C32 O31  SING N N 31 
A1AEP N33 C32  SING N N 32 
A1AEP C34 N33  SING Y N 33 
A1AEP C36 N35  DOUB Y N 34 
A1AEP N37 C36  SING Y N 35 
A1AEP C38 N37  DOUB Y N 36 
A1AEP N39 C38  SING N N 37 
A1AEP N35 C34  SING Y N 38 
A1AEP C40 C34  DOUB Y N 39 
A1AEP N41 C40  SING Y N 40 
A1AEP C42 N41  DOUB Y N 41 
A1AEP C02 C32  SING N N 42 
A1AEP P05 O28  SING N N 43 
A1AEP C13 C26  SING N N 44 
A1AEP N17 C22  SING N N 45 
A1AEP N33 C42  SING Y N 46 
A1AEP C38 C40  SING Y N 47 
A1AEP C13 H131 SING N N 48 
A1AEP C21 H211 SING N N 49 
A1AEP C22 H221 SING N N 50 
A1AEP C26 H261 SING N N 51 
A1AEP C02 H021 SING N N 52 
A1AEP C03 H031 SING N N 53 
A1AEP C08 H081 SING N N 54 
A1AEP C09 H091 SING N N 55 
A1AEP C09 H092 SING N N 56 
A1AEP C14 H141 SING N N 57 
A1AEP C16 H161 SING N N 58 
A1AEP C27 H272 SING N N 59 
A1AEP C27 H271 SING N N 60 
A1AEP C32 H321 SING N N 61 
A1AEP C36 H361 SING N N 62 
A1AEP C42 H421 SING N N 63 
A1AEP N19 H191 SING N N 64 
A1AEP N39 H391 SING N N 65 
A1AEP N39 H392 SING N N 66 
A1AEP O01 H011 SING N N 67 
A1AEP O07 H1   SING N N 68 
A1AEP O15 H151 SING N N 69 
A1AEP O30 H2   SING N N 70 
# 
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 
A1AEP SMILES           ACDLabs              12.01 "Nc1ncnc2c1ncn2C1OC2COP(=O)(O)OC3C(COP(=O)(O)OC2C1O)OC(C3O)N1C=CC(=O)NC1=O"                                                                                                                                                                                                         
A1AEP InChI            InChI                1.06  "InChI=1S/C19H23N7O14P2/c20-15-10-16(22-5-21-15)26(6-23-10)18-12(29)14-8(38-18)4-36-41(31,32)39-13-7(3-35-42(33,34)40-14)37-17(11(13)28)25-2-1-9(27)24-19(25)30/h1-2,5-8,11-14,17-18,28-29H,3-4H2,(H,31,32)(H,33,34)(H2,20,21,22)(H,24,27,30)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1" 
A1AEP InChIKey         InChI                1.06  CYVLWDUVMGUTIY-KPKSGTNCSA-N                                                                                                                                                                                                                                                         
A1AEP SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[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)N6C=CC(=O)NC6=O"                                                                                                                                                              
A1AEP SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)N6C=CC(=O)NC6=O"                                                                                                                                                                           
A1AEP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@@H]5O)N6C=CC(=O)NC6=O)O)O)N"                                                                                                                                                           
A1AEP SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)N6C=CC(=O)NC6=O)O)O)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 
A1AEP "SYSTEMATIC NAME" ACDLabs              12.01 "1-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxooctahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]pyrimidine-2,4(1H,3H)-dione" 
A1AEP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(1~{S},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-17-(6-aminopurin-9-yl)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]pyrimidine-2,4-dione"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1AEP "Create component"   2024-02-13 RCSB 
A1AEP "Modify coordinates" 2025-05-12 RCSB 
A1AEP "Initial release"    2025-05-21 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1AEP 
_pdbx_chem_comp_synonyms.name         "1-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxooctahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]pyrimidine-2,4(1H,3H)-dione" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
