data_CX2 # _chem_comp.id CX2 _chem_comp.name "2'-deoxy-5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H19 N4 O6 P S" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-10-01 _chem_comp.pdbx_modified_date 2012-01-06 _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 366.331 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CX2 _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 3JY2 _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 CX2 P P P 0 1 N N N -4.876 57.787 16.749 -3.499 1.000 -0.066 P CX2 1 CX2 S S S 0 1 N N N -2.868 53.060 16.065 -3.166 -4.167 0.460 S CX2 2 CX2 N1 N1 N 0 1 N N N -1.468 58.384 19.818 3.100 0.031 0.597 N1 CX2 3 CX2 C2 C2 C 0 1 N N N -1.557 58.292 21.222 3.001 -0.400 -0.674 C2 CX2 4 CX2 O2 O2 O 0 1 N N N -1.690 59.311 21.905 2.212 0.140 -1.431 O2 CX2 5 CX2 N3 N3 N 0 1 N N N -1.493 57.033 21.844 3.752 -1.406 -1.119 N3 CX2 6 CX2 C4 C4 C 0 1 N N N -1.343 55.873 21.072 4.619 -2.011 -0.317 C4 CX2 7 CX2 N4 N4 N 0 1 N N N -1.283 54.687 21.672 5.389 -3.049 -0.788 N4 CX2 8 CX2 C5 C5 C 0 1 N N N -1.256 55.967 19.680 4.746 -1.584 1.020 C5 CX2 9 CX2 C6 C6 C 0 1 N N N -1.321 57.211 19.052 3.976 -0.559 1.458 C6 CX2 10 CX2 "C1'" "C1'" C 0 1 N N R -1.552 59.725 19.173 2.266 1.144 1.056 "C1'" CX2 11 CX2 "C2'" "C2'" C 0 1 N N N -1.186 59.811 17.693 2.650 2.433 0.303 "C2'" CX2 12 CX2 "C3'" "C3'" C 0 1 N N S -2.010 61.016 17.228 1.338 2.873 -0.390 "C3'" CX2 13 CX2 "O3'" "O3'" O 0 1 N N N -1.432 62.253 17.636 1.169 4.290 -0.309 "O3'" CX2 14 CX2 "C4'" "C4'" C 0 1 N N R -3.283 60.900 18.059 0.264 2.140 0.453 "C4'" CX2 15 CX2 "N4'" "N4'" N 0 1 N N N -4.425 56.796 15.549 -3.433 -0.393 -1.008 "N4'" CX2 16 CX2 "O4'" "O4'" O 0 1 N N N -2.964 60.050 19.212 0.885 0.874 0.762 "O4'" CX2 17 CX2 "C5'" "C5'" C 0 1 N N N -4.395 60.286 17.224 -1.012 1.929 -0.365 "C5'" CX2 18 CX2 "O5'" "O5'" O 0 1 N N N -3.967 59.074 16.608 -2.023 1.357 0.468 "O5'" CX2 19 CX2 "C7'" "C7'" C 0 1 N N N -4.468 55.332 15.692 -2.925 -1.531 -0.231 "C7'" CX2 20 CX2 "C8'" "C8'" C 0 1 N N N -3.053 54.790 15.487 -3.794 -2.761 -0.500 "C8'" CX2 21 CX2 OP1 OP1 O 0 1 N N N -6.303 58.125 16.650 -4.015 2.123 -0.880 OP1 CX2 22 CX2 HS HS H 0 1 N N N -1.619 52.818 15.798 -4.011 -5.160 0.130 HS CX2 23 CX2 HN4 HN4 H 0 1 N N N -1.345 54.627 22.668 5.299 -3.340 -1.709 HN4 CX2 24 CX2 HN4A HN4A H 0 0 N N N -1.176 53.856 21.127 6.022 -3.489 -0.199 HN4A CX2 25 CX2 H5 H5 H 0 1 N N N -1.138 55.072 19.088 5.447 -2.066 1.686 H5 CX2 26 CX2 H6 H6 H 0 1 N N N -1.258 57.275 17.976 4.056 -0.213 2.478 H6 CX2 27 CX2 "H1'" "H1'" H 0 1 N N N -0.842 60.374 19.707 2.398 1.289 2.128 "H1'" CX2 28 CX2 "H2'" "H2'" H 0 1 N N N -0.107 59.967 17.543 2.988 3.197 1.002 "H2'" CX2 29 CX2 "H2'A" "H2'A" H 0 0 N N N -1.454 58.894 17.148 3.422 2.225 -0.439 "H2'A" CX2 30 CX2 "H3'" "H3'" H 0 1 N N N -2.115 61.011 16.133 1.314 2.539 -1.427 "H3'" CX2 31 CX2 "HO3'" "HO3'" H 0 0 N N N -1.972 62.972 17.329 1.869 4.795 -0.746 "HO3'" CX2 32 CX2 "H4'" "H4'" H 0 1 N N N -3.632 61.887 18.395 0.048 2.694 1.366 "H4'" CX2 33 CX2 "HN4'" "HN4'" H 0 0 N N N -5.033 57.008 14.784 -4.336 -0.602 -1.408 "HN4'" CX2 34 CX2 "H5'" "H5'" H 0 1 N N N -5.253 60.070 17.877 -1.358 2.887 -0.752 "H5'" CX2 35 CX2 "H5'A" "H5'A" H 0 0 N N N -4.688 61.000 16.440 -0.803 1.255 -1.197 "H5'A" CX2 36 CX2 "H7'" "H7'" H 0 1 N N N -4.829 55.064 16.696 -1.896 -1.741 -0.525 "H7'" CX2 37 CX2 "H7'A" "H7'A" H 0 0 N N N -5.146 54.902 14.940 -2.957 -1.289 0.831 "H7'A" CX2 38 CX2 "H8'" "H8'" H 0 1 N N N -2.353 55.422 16.053 -3.761 -3.004 -1.562 "H8'" CX2 39 CX2 "H8'A" "H8'A" H 0 0 N N N -2.820 54.824 14.412 -4.822 -2.551 -0.206 "H8'A" CX2 40 CX2 OP3 OP3 O 0 1 N Y N -5.167 57.118 18.307 -4.478 0.753 1.189 O6 CX2 41 CX2 HOP3 HOP3 H 0 0 N Y N -6.088 57.205 18.523 -4.201 0.030 1.768 H19 CX2 42 # 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 CX2 P "N4'" SING N N 1 CX2 P "O5'" SING N N 2 CX2 P OP1 DOUB N N 3 CX2 S "C8'" SING N N 4 CX2 S HS SING N N 5 CX2 N1 C2 SING N N 6 CX2 N1 C6 SING N N 7 CX2 N1 "C1'" SING N N 8 CX2 C2 O2 DOUB N N 9 CX2 C2 N3 SING N N 10 CX2 N3 C4 DOUB N N 11 CX2 C4 N4 SING N N 12 CX2 C4 C5 SING N N 13 CX2 N4 HN4 SING N N 14 CX2 N4 HN4A SING N N 15 CX2 C5 C6 DOUB N N 16 CX2 C5 H5 SING N N 17 CX2 C6 H6 SING N N 18 CX2 "C1'" "C2'" SING N N 19 CX2 "C1'" "O4'" SING N N 20 CX2 "C1'" "H1'" SING N N 21 CX2 "C2'" "C3'" SING N N 22 CX2 "C2'" "H2'" SING N N 23 CX2 "C2'" "H2'A" SING N N 24 CX2 "C3'" "O3'" SING N N 25 CX2 "C3'" "C4'" SING N N 26 CX2 "C3'" "H3'" SING N N 27 CX2 "O3'" "HO3'" SING N N 28 CX2 "C4'" "O4'" SING N N 29 CX2 "C4'" "C5'" SING N N 30 CX2 "C4'" "H4'" SING N N 31 CX2 "N4'" "C7'" SING N N 32 CX2 "N4'" "HN4'" SING N N 33 CX2 "C5'" "O5'" SING N N 34 CX2 "C5'" "H5'" SING N N 35 CX2 "C5'" "H5'A" SING N N 36 CX2 "C7'" "C8'" SING N N 37 CX2 "C7'" "H7'" SING N N 38 CX2 "C7'" "H7'A" SING N N 39 CX2 "C8'" "H8'" SING N N 40 CX2 "C8'" "H8'A" SING N N 41 CX2 P OP3 SING N N 42 CX2 OP3 HOP3 SING N N 43 # 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 CX2 SMILES ACDLabs 11.02 "O=P(O)(OCC2OC(N1C(=O)N=C(N)C=C1)CC2O)NCCS" CX2 SMILES_CANONICAL CACTVS 3.352 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2" CX2 SMILES CACTVS 3.352 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2" CX2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(NCCS)O)O" CX2 SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NCCS)O)O" CX2 InChI InChI 1.03 "InChI=1S/C11H19N4O6PS/c12-9-1-3-15(11(17)14-9)10-5-7(16)8(21-10)6-20-22(18,19)13-2-4-23/h1,3,7-8,10,16,23H,2,4-6H2,(H2,12,14,17)(H2,13,18,19)/t7-,8+,10+/m0/s1" CX2 InChIKey InChI 1.03 UBFVQIIQWMOGNR-QXFUBDJGSA-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 CX2 "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine" CX2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CX2 "Create component" 2009-10-01 RCSB CX2 "Modify descriptor" 2011-06-04 RCSB #