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 ? #