data_CPA # _chem_comp.id CPA _chem_comp.name "2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H25 N8 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _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 540.424 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CPA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1RPG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 CPA P P P 0 1 N N R N N N 29.672 17.229 5.732 -1.233 -0.102 0.977 P CPA 1 CPA O1P O1P O 0 1 N N N N N N 30.011 17.950 6.971 -2.410 -0.840 1.486 O1P CPA 2 CPA O2P O2P O 0 1 N N N N N N 28.375 17.414 5.056 0.052 -1.071 0.982 O2P CPA 3 CPA O5D "CO5'" O 0 1 N N N N N N 33.553 14.187 5.073 -3.819 1.223 5.310 O5D CPA 4 CPA C5X "CC5'" C 0 1 N N N N N N 32.462 13.299 4.923 -2.975 0.588 4.348 C5X CPA 5 CPA C4X "CC4'" C 0 1 N N R N N N 31.350 13.662 5.866 -1.639 1.330 4.272 C4X CPA 6 CPA O4D "CO4'" O 0 1 N N N N N N 31.440 12.903 7.083 -0.913 1.207 5.516 O4D CPA 7 CPA C3X "CC3'" C 0 1 N N S N N N 31.225 15.114 6.247 -0.701 0.663 3.235 C3X CPA 8 CPA O3D "CO3'" O 0 1 N N N N N N 29.966 15.692 5.896 -0.949 1.170 1.922 O3D CPA 9 CPA C2X "CC2'" C 0 1 N N N N N N 31.499 15.151 7.727 0.697 1.093 3.738 C2X CPA 10 CPA C1X "CC1'" C 0 1 N N R N N N 31.287 13.731 8.220 0.470 1.459 5.218 C1X CPA 11 CPA N1C CN1 N 0 1 N N N N N N 32.294 13.362 9.246 1.323 0.630 6.073 N1C CPA 12 CPA CC2 CC2 C 0 1 N N N N N N 31.937 13.672 10.537 1.198 -0.709 6.045 CC2 CPA 13 CPA N3C CN3 N 0 1 N N N N N N 32.813 13.368 11.505 1.961 -1.486 6.812 N3C CPA 14 CPA CC4 CC4 C 0 1 N N N N N N 33.977 12.802 11.279 2.866 -0.957 7.625 CC4 CPA 15 CPA CC5 CC5 C 0 1 N N N N N N 34.372 12.470 9.933 3.018 0.443 7.681 CC5 CPA 16 CPA CC6 CC6 C 0 1 N N N N N N 33.509 12.766 8.954 2.239 1.219 6.892 CC6 CPA 17 CPA O2C CO2 O 0 1 N N N N N N 30.850 14.210 10.691 0.373 -1.219 5.306 O2C CPA 18 CPA N4C CN4 N 0 1 N N N N N N 34.789 12.535 12.303 3.648 -1.770 8.413 N4C CPA 19 CPA O5B "AO5'" O 0 1 N N N N N N 30.775 17.682 4.616 -1.521 0.398 -0.525 O5B CPA 20 CPA C5B "AC5'" C 0 1 N N N N N N 30.571 17.371 3.249 -1.765 -0.769 -1.310 C5B CPA 21 CPA C4B "AC4'" C 0 1 N N R N N N 30.276 18.599 2.429 -2.047 -0.361 -2.757 C4B CPA 22 CPA O4B "AO4'" O 0 1 N N N N N N 31.302 19.603 2.627 -0.891 0.275 -3.341 O4B CPA 23 CPA C3B "AC3'" C 0 1 N N S N N N 30.199 18.375 0.925 -2.261 -1.614 -3.645 C3B CPA 24 CPA O3B "AO3'" O 0 1 N N N N N N 29.140 19.160 0.367 -3.623 -2.045 -3.609 O3B CPA 25 CPA C2B "AC2'" C 0 1 N N N N N N 31.570 18.831 0.441 -1.888 -1.079 -5.052 C2B CPA 26 CPA C1B "AC1'" C 0 1 N N R N N N 31.829 20.006 1.374 -1.026 0.165 -4.768 C1B CPA 27 CPA N9A AN9 N 0 1 Y N N N N N 33.263 20.283 1.573 0.293 0.012 -5.383 N9A CPA 28 CPA C8A AC8 C 0 1 Y N N N N N 34.321 19.435 1.723 1.391 -0.552 -4.806 C8A CPA 29 CPA N7A AN7 N 0 1 Y N N N N N 35.462 20.083 1.890 2.394 -0.523 -5.636 N7A CPA 30 CPA C5A AC5 C 0 1 Y N N N N N 35.107 21.434 1.842 2.004 0.059 -6.795 C5A CPA 31 CPA C6A AC6 C 0 1 Y N N N N N 35.912 22.606 1.951 2.636 0.356 -8.014 C6A CPA 32 CPA N6A AN6 N 0 1 N N N N N N 37.219 22.598 2.137 3.967 0.034 -8.218 N6A CPA 33 CPA N1A AN1 N 0 1 Y N N N N N 35.253 23.809 1.861 1.927 0.953 -8.966 N1A CPA 34 CPA C2A AC2 C 0 1 Y N N N N N 33.943 23.768 1.672 0.658 1.264 -8.780 C2A CPA 35 CPA N3A AN3 N 0 1 Y N N N N N 33.106 22.738 1.553 0.024 1.005 -7.656 N3A CPA 36 CPA C4A AC4 C 0 1 Y N N N N N 33.738 21.566 1.646 0.649 0.405 -6.649 C4A CPA 37 CPA HOP2 2HOP H 0 0 N N N N N N 28.156 16.949 4.256 0.794 -0.552 0.645 HOP2 CPA 38 CPA HO5C CHO5 H 0 0 N N N N N N 34.256 13.957 4.476 -4.648 0.725 5.327 HO5C CPA 39 CPA H51C CH51 H 0 0 N N N N N N 32.109 13.251 3.866 -3.458 0.608 3.371 H51C CPA 40 CPA H52C CH52 H 0 0 N N N N N N 32.774 12.235 5.042 -2.799 -0.445 4.645 H52C CPA 41 CPA H4D "CH4'" H 0 1 N N N N N N 30.440 13.416 5.269 -1.799 2.380 4.026 H4D CPA 42 CPA H3D "CH3'" H 0 1 N N N N N N 31.948 15.742 5.677 -0.806 -0.421 3.257 H3D CPA 43 CPA H21C CH21 H 0 0 N N N N N N 32.499 15.569 7.985 1.053 1.959 3.181 H21C CPA 44 CPA H22C CH22 H 0 0 N N N N N N 30.892 15.909 8.274 1.403 0.267 3.654 H22C CPA 45 CPA H1D "CH1'" H 0 1 N N N N N N 30.283 13.621 8.693 0.697 2.513 5.378 H1D CPA 46 CPA H5C CH5 H 0 1 N N N N N N 35.326 11.993 9.654 3.750 0.889 8.338 H5C CPA 47 CPA H6C CH6 H 0 1 N N N N N N 33.796 12.521 7.917 2.340 2.294 6.914 H6C CPA 48 CPA H41C CH41 H 0 0 N N N N N N 35.692 12.095 12.127 3.538 -2.733 8.375 H41C CPA 49 CPA H42C CH42 H 0 0 N N N N N N 34.279 11.970 12.983 4.311 -1.381 9.003 H42C CPA 50 CPA H51A AH51 H 0 0 N N N N N N 31.434 16.802 2.830 -0.888 -1.417 -1.279 H51A CPA 51 CPA H52A AH52 H 0 0 N N N N N N 29.775 16.600 3.123 -2.625 -1.304 -0.909 H52A CPA 52 CPA H4B "AH4'" H 0 1 N N N N N N 29.270 18.917 2.790 -2.914 0.296 -2.807 H4B CPA 53 CPA H3B "AH3'" H 0 1 N N N N N N 29.976 17.323 0.628 -1.591 -2.419 -3.345 H3B CPA 54 CPA HO3A AHO3 H 0 0 N N N N N N 29.092 19.020 -0.571 -3.705 -2.765 -4.249 HO3A CPA 55 CPA H21A AH21 H 0 0 N N N N N N 32.360 18.044 0.428 -2.787 -0.804 -5.603 H21A CPA 56 CPA H22A AH22 H 0 0 N N N N N N 31.643 19.058 -0.648 -1.314 -1.823 -5.604 H22A CPA 57 CPA H1B "AH1'" H 0 1 N N N N N N 31.371 20.927 0.943 -1.519 1.054 -5.163 H1B CPA 58 CPA H8A AH8 H 0 1 N N N N N N 34.259 18.333 1.710 1.425 -0.962 -3.808 H8A CPA 59 CPA H61A AH61 H 0 0 N N N N N N 37.794 23.436 2.215 4.392 0.244 -9.064 H61A CPA 60 CPA H62A AH62 H 0 0 N N N N N N 37.621 22.029 1.392 4.473 -0.401 -7.515 H62A CPA 61 CPA H2A AH2 H 0 1 N N N N N N 33.468 24.761 1.601 0.119 1.749 -9.581 H2A CPA 62 # 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 CPA P O1P DOUB N N 1 CPA P O2P SING N N 2 CPA P O3D SING N N 3 CPA P O5B SING N N 4 CPA O2P HOP2 SING N N 5 CPA O5D C5X SING N N 6 CPA O5D HO5C SING N N 7 CPA C5X C4X SING N N 8 CPA C5X H51C SING N N 9 CPA C5X H52C SING N N 10 CPA C4X O4D SING N N 11 CPA C4X C3X SING N N 12 CPA C4X H4D SING N N 13 CPA O4D C1X SING N N 14 CPA C3X O3D SING N N 15 CPA C3X C2X SING N N 16 CPA C3X H3D SING N N 17 CPA C2X C1X SING N N 18 CPA C2X H21C SING N N 19 CPA C2X H22C SING N N 20 CPA C1X N1C SING N N 21 CPA C1X H1D SING N N 22 CPA N1C CC2 SING N N 23 CPA N1C CC6 SING N N 24 CPA CC2 N3C SING N N 25 CPA CC2 O2C DOUB N N 26 CPA N3C CC4 DOUB N N 27 CPA CC4 CC5 SING N N 28 CPA CC4 N4C SING N N 29 CPA CC5 CC6 DOUB N N 30 CPA CC5 H5C SING N N 31 CPA CC6 H6C SING N N 32 CPA N4C H41C SING N N 33 CPA N4C H42C SING N N 34 CPA O5B C5B SING N N 35 CPA C5B C4B SING N N 36 CPA C5B H51A SING N N 37 CPA C5B H52A SING N N 38 CPA C4B O4B SING N N 39 CPA C4B C3B SING N N 40 CPA C4B H4B SING N N 41 CPA O4B C1B SING N N 42 CPA C3B O3B SING N N 43 CPA C3B C2B SING N N 44 CPA C3B H3B SING N N 45 CPA O3B HO3A SING N N 46 CPA C2B C1B SING N N 47 CPA C2B H21A SING N N 48 CPA C2B H22A SING N N 49 CPA C1B N9A SING N N 50 CPA C1B H1B SING N N 51 CPA N9A C8A SING Y N 52 CPA N9A C4A SING Y N 53 CPA C8A N7A DOUB Y N 54 CPA C8A H8A SING N N 55 CPA N7A C5A SING Y N 56 CPA C5A C6A SING Y N 57 CPA C5A C4A DOUB Y N 58 CPA C6A N6A SING N N 59 CPA C6A N1A DOUB Y N 60 CPA N6A H61A SING N N 61 CPA N6A H62A SING N N 62 CPA N1A C2A SING Y N 63 CPA C2A N3A DOUB Y N 64 CPA C2A H2A SING N N 65 CPA N3A C4A SING Y N 66 # 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 CPA SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C5OC(CO)C(OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)CC4O)C5" CPA SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O[P@@](O)(=O)OC[C@H]3O[C@H](C[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](CO)O2" CPA SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O[P](O)(=O)OC[CH]3O[CH](C[CH]3O)n4cnc5c(N)ncnc45)[CH](CO)O2" CPA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[C@H]4C[C@@H](O[C@@H]4CO)N5C=CC(=NC5=O)N)O)N" CPA SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OC4CC(OC4CO)N5C=CC(=NC5=O)N)O)N" CPA InChI InChI 1.03 "InChI=1S/C19H25N8O9P/c20-13-1-2-26(19(30)25-13)15-4-10(11(5-28)34-15)36-37(31,32)33-6-12-9(29)3-14(35-12)27-8-24-16-17(21)22-7-23-18(16)27/h1-2,7-12,14-15,28-29H,3-6H2,(H,31,32)(H2,20,25,30)(H2,21,22,23)/t9-,10-,11+,12+,14+,15+/m0/s1" CPA InChIKey InChI 1.03 LYWWDKIADIGKTH-IDMWBNCISA-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 CPA "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-2-(hydroxymethyl)tetrahydrofuran-3-yl [(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methyl hydrogen (R)-phosphate (non-preferred name)" CPA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl] [(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CPA "Create component" 1999-07-08 RCSB CPA "Modify descriptor" 2011-06-04 RCSB CPA "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id CPA _pdbx_chem_comp_pcm.modified_residue_id GLN _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom N6A _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE1 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #