data_CJ1 # _chem_comp.id CJ1 _chem_comp.name "7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H14 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-22 _chem_comp.pdbx_modified_date 2018-09-14 _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 347.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CJ1 _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 6B1Q _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 CJ1 C2 C1 C 0 1 Y N N 20.609 4.638 -11.728 4.945 0.703 0.918 C2 CJ1 1 CJ1 C4 C2 C 0 1 Y N N 21.224 5.327 -9.721 2.928 -0.062 0.108 C4 CJ1 2 CJ1 C5 C3 C 0 1 Y N N 21.928 6.425 -10.169 3.587 -1.202 -0.389 C5 CJ1 3 CJ1 C6 C4 C 0 1 Y N N 21.979 6.664 -11.576 4.967 -1.330 -0.179 C6 CJ1 4 CJ1 C7 C5 C 0 1 Y N N 22.476 7.114 -9.087 2.559 -2.019 -1.034 C7 CJ1 5 CJ1 P P1 P 0 1 N N N 18.840 7.706 -4.384 -5.068 -0.817 0.347 P CJ1 6 CJ1 OP1 O1 O 0 1 N N N 17.842 7.549 -3.296 -5.025 -1.710 -0.832 OP1 CJ1 7 CJ1 "O5'" O2 O 0 1 N N N 19.260 6.250 -4.843 -3.642 -0.089 0.521 "O5'" CJ1 8 CJ1 "C5'" C6 C 0 1 N N N 18.225 5.353 -5.286 -3.025 0.671 -0.520 "C5'" CJ1 9 CJ1 "C4'" C7 C 0 1 N N R 18.817 4.233 -6.101 -1.686 1.222 -0.024 "C4'" CJ1 10 CJ1 "C3'" C8 C 0 1 N N S 19.974 3.472 -5.450 -1.059 2.149 -1.088 "C3'" CJ1 11 CJ1 "O3'" O3 O 0 1 N N N 19.828 2.133 -5.923 -1.328 3.519 -0.779 "O3'" CJ1 12 CJ1 "C2'" C9 C 0 1 N N N 21.207 4.121 -6.069 0.455 1.858 -0.994 "C2'" CJ1 13 CJ1 "C1'" C10 C 0 1 N N R 20.708 4.327 -7.488 0.564 0.788 0.115 "C1'" CJ1 14 CJ1 "O4'" O4 O 0 1 N N N 19.344 4.725 -7.355 -0.732 0.150 0.141 "O4'" CJ1 15 CJ1 N9 N1 N 0 1 Y N N 21.336 5.333 -8.349 1.606 -0.187 -0.216 N9 CJ1 16 CJ1 C8 C11 C 0 1 Y N N 22.100 6.434 -8.034 1.398 -1.359 -0.898 C8 CJ1 17 CJ1 N3 N2 N 0 1 Y N N 20.546 4.400 -10.431 3.645 0.858 0.751 N3 CJ1 18 CJ1 O2 O5 O 0 1 N N N 19.994 3.825 -12.597 5.637 1.663 1.579 O2 CJ1 19 CJ1 N1 N3 N 0 1 Y N N 21.275 5.698 -12.282 5.600 -0.359 0.469 N1 CJ1 20 CJ1 O6 O6 O 0 1 N N N 22.536 7.573 -12.212 5.641 -2.410 -0.639 O6 CJ1 21 CJ1 OP2 O7 O 0 1 N N N 20.078 8.504 -4.152 -6.215 0.293 0.139 OP2 CJ1 22 CJ1 H1 H1 H 0 1 N N N 23.078 8.011 -9.113 2.706 -2.969 -1.527 H1 CJ1 23 CJ1 H3 H3 H 0 1 N N N 17.503 5.908 -5.903 -2.856 0.031 -1.386 H3 CJ1 24 CJ1 H4 H4 H 0 1 N N N 17.711 4.931 -4.410 -3.676 1.498 -0.801 H4 CJ1 25 CJ1 H5 H5 H 0 1 N N N 18.017 3.508 -6.313 -1.822 1.759 0.915 H5 CJ1 26 CJ1 H6 H6 H 0 1 N N N 19.963 3.560 -4.354 -1.435 1.901 -2.080 H6 CJ1 27 CJ1 H7 H7 H 0 1 N N N 20.518 1.591 -5.559 -0.956 4.145 -1.416 H7 CJ1 28 CJ1 H8 H8 H 0 1 N N N 22.081 3.453 -6.036 0.828 1.465 -1.940 H8 CJ1 29 CJ1 H9 H9 H 0 1 N N N 21.456 5.075 -5.581 1.001 2.758 -0.714 H9 CJ1 30 CJ1 H10 H10 H 0 1 N N N 20.748 3.355 -8.002 0.775 1.258 1.076 H10 CJ1 31 CJ1 H11 H11 H 0 1 N N N 22.362 6.708 -7.023 0.443 -1.700 -1.270 H11 CJ1 32 CJ1 H14 H14 H 0 1 N N N 20.076 8.842 -3.264 -6.300 0.914 0.875 H14 CJ1 33 CJ1 OP3 O8 O 0 1 N Y N 18.107 8.296 -5.662 -5.392 -1.683 1.665 OP3 CJ1 34 CJ1 "HO3'" H2 H 0 0 N Y N 17.186 8.426 -5.468 -6.238 -2.151 1.630 "HO3'" CJ1 35 CJ1 H2 H13 H 0 1 N N N 20.135 4.141 -13.482 5.689 1.523 2.534 H2 CJ1 36 CJ1 H12 H12 H 0 1 N N N 22.380 7.452 -13.141 5.991 -2.304 -1.534 H12 CJ1 37 # 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 CJ1 O2 C2 SING N N 1 CJ1 N1 C2 SING Y N 2 CJ1 N1 C6 DOUB Y N 3 CJ1 O6 C6 SING N N 4 CJ1 C2 N3 DOUB Y N 5 CJ1 C6 C5 SING Y N 6 CJ1 N3 C4 SING Y N 7 CJ1 C5 C4 DOUB Y N 8 CJ1 C5 C7 SING Y N 9 CJ1 C4 N9 SING Y N 10 CJ1 C7 C8 DOUB Y N 11 CJ1 N9 C8 SING Y N 12 CJ1 N9 "C1'" SING N N 13 CJ1 "C1'" "O4'" SING N N 14 CJ1 "C1'" "C2'" SING N N 15 CJ1 "O4'" "C4'" SING N N 16 CJ1 "C4'" "C3'" SING N N 17 CJ1 "C4'" "C5'" SING N N 18 CJ1 "C2'" "C3'" SING N N 19 CJ1 "O3'" "C3'" SING N N 20 CJ1 "C5'" "O5'" SING N N 21 CJ1 "O5'" P SING N N 22 CJ1 P OP2 SING N N 23 CJ1 P OP1 DOUB N N 24 CJ1 C7 H1 SING N N 25 CJ1 "C5'" H3 SING N N 26 CJ1 "C5'" H4 SING N N 27 CJ1 "C4'" H5 SING N N 28 CJ1 "C3'" H6 SING N N 29 CJ1 "O3'" H7 SING N N 30 CJ1 "C2'" H8 SING N N 31 CJ1 "C2'" H9 SING N N 32 CJ1 "C1'" H10 SING N N 33 CJ1 C8 H11 SING N N 34 CJ1 OP2 H14 SING N N 35 CJ1 P OP3 SING N N 36 CJ1 OP3 "HO3'" SING N N 37 CJ1 O2 H2 SING N N 38 CJ1 O6 H12 SING N N 39 # 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 CJ1 SMILES ACDLabs 12.01 "c3(nc2n(C1CC(C(COP(O)(=O)O)O1)O)ccc2c(n3)O)O" CJ1 InChI InChI 1.03 "InChI=1S/C11H14N3O8P/c15-6-3-8(22-7(6)4-21-23(18,19)20)14-2-1-5-9(14)12-11(17)13-10(5)16/h1-2,6-8,15H,3-4H2,(H2,18,19,20)(H2,12,13,16,17)/t6-,7+,8+/m0/s1" CJ1 InChIKey InChI 1.03 KGLSEDQJBHBOAW-XLPZGREQSA-N CJ1 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccc3c(O)nc(O)nc23" CJ1 SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccc3c(O)nc(O)nc23" CJ1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cn(c2c1c(nc(n2)O)O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" CJ1 SMILES "OpenEye OEToolkits" 2.0.6 "c1cn(c2c1c(nc(n2)O)O)C3CC(C(O3)COP(=O)(O)O)O" # 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 CJ1 "SYSTEMATIC NAME" ACDLabs 12.01 "7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diol" CJ1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 CJ1 "Create component" 2017-09-22 RCSB CJ1 "Modify linking type" 2017-09-22 RCSB CJ1 "Initial release" 2018-09-19 RCSB #