data_C38 # _chem_comp.id C38 _chem_comp.name "5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 I N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1997-03-12 _chem_comp.pdbx_modified_date 2011-06-04 _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 433.094 _chem_comp.one_letter_code C _chem_comp.three_letter_code C38 _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 1MEY _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 C38 O3P O3P O 0 1 N Y N 35.430 28.740 22.370 2.703 -0.834 -6.042 O3P C38 1 C38 P P P 0 1 N N N 34.648 29.964 22.731 1.357 -0.068 -5.602 P C38 2 C38 O1P O1P O 0 1 N N N 34.885 30.675 24.020 1.681 1.328 -5.236 O1P C38 3 C38 O2P O2P O 0 1 N N N 34.881 31.135 21.669 0.312 -0.073 -6.827 O2P C38 4 C38 "O5'" O5* O 0 1 N N N 33.107 29.604 22.591 0.703 -0.816 -4.336 "O5'" C38 5 C38 "C5'" C5* C 0 1 N N N 32.155 30.630 22.551 -0.481 -0.093 -3.995 "C5'" C38 6 C38 "C4'" C4* C 0 1 N N R 30.995 30.222 21.679 -1.155 -0.756 -2.793 "C4'" C38 7 C38 "O4'" O4* O 0 1 N N N 31.297 30.390 20.271 -0.324 -0.647 -1.615 "O4'" C38 8 C38 "C3'" C3* C 0 1 N N S 30.561 28.776 21.837 -2.445 0.007 -2.400 "C3'" C38 9 C38 "O3'" O3* O 0 1 N N N 29.175 28.764 22.087 -3.563 -0.453 -3.160 "O3'" C38 10 C38 "C2'" C2* C 0 1 N N N 30.796 28.167 20.469 -2.601 -0.365 -0.906 "C2'" C38 11 C38 "C1'" C1* C 0 1 N N R 30.644 29.370 19.562 -1.188 -0.808 -0.478 "C1'" C38 12 C38 N1 N1 N 0 1 N N N 31.296 29.221 18.243 -0.717 0.027 0.628 N1 C38 13 C38 C2 C2 C 0 1 N N N 30.567 29.595 17.096 -0.605 1.358 0.461 C2 C38 14 C38 O2 O2 O 0 1 N N N 29.433 30.100 17.227 -0.897 1.854 -0.614 O2 C38 15 C38 N3 N3 N 0 1 N N N 31.101 29.396 15.880 -0.179 2.142 1.449 N3 C38 16 C38 C4 C4 C 0 1 N N N 32.319 28.851 15.751 0.144 1.629 2.629 C4 C38 17 C38 N4 N4 N 0 1 N N N 32.756 28.691 14.482 0.582 2.449 3.643 N4 C38 18 C38 C5 C5 C 0 1 N N N 33.117 28.465 16.912 0.043 0.238 2.836 C5 C38 19 C38 C6 C6 C 0 1 N N N 32.562 28.691 18.121 -0.396 -0.545 1.822 C6 C38 20 C38 I I I 0 1 N N N 34.489 27.845 16.746 0.548 -0.601 4.687 I C38 21 C38 H3P H3P H 0 1 N N N 35.279 28.287 21.548 3.062 -0.355 -6.801 H3P C38 22 C38 H2P H2P H 0 1 N N N 34.384 31.911 21.898 0.128 -0.999 -7.034 H2P C38 23 C38 "H5'1" 1H5* H 0 0 N N N 32.599 31.601 22.229 -1.166 -0.097 -4.844 "H5'1" C38 24 C38 "H5'2" 2H5* H 0 0 N N N 31.824 30.934 23.572 -0.219 0.934 -3.745 "H5'2" C38 25 C38 "H4'" H4* H 0 1 N N N 30.126 30.875 21.928 -1.378 -1.801 -3.007 "H4'" C38 26 C38 "H3'" H3* H 0 1 N N N 31.136 28.250 22.635 -2.312 1.083 -2.521 "H3'" C38 27 C38 HA HA H 0 1 N N N 28.903 27.859 22.186 -4.345 -0.008 -2.806 HA C38 28 C38 "H2'1" 1H2* H 0 0 N N N 30.141 27.300 20.218 -3.310 -1.184 -0.789 "H2'1" C38 29 C38 "H2'2" 2H2* H 0 0 N N N 31.755 27.609 20.358 -2.920 0.501 -0.327 "H2'2" C38 30 C38 "H1'" H1* H 0 1 N N N 29.565 29.621 19.432 -1.206 -1.854 -0.170 "H1'" C38 31 C38 H4N1 1H4N H 0 0 N N N 33.683 28.276 14.384 0.655 3.405 3.496 H4N1 C38 32 C38 H4N2 2H4N H 0 0 N N N 32.199 28.961 13.671 0.815 2.072 4.506 H4N2 C38 33 C38 H6 H6 H 0 1 N N N 33.149 28.439 19.019 -0.486 -1.613 1.957 H6 C38 34 # 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 C38 O3P P SING N N 1 C38 O3P H3P SING N N 2 C38 P O1P DOUB N N 3 C38 P O2P SING N N 4 C38 P "O5'" SING N N 5 C38 O2P H2P SING N N 6 C38 "O5'" "C5'" SING N N 7 C38 "C5'" "C4'" SING N N 8 C38 "C5'" "H5'1" SING N N 9 C38 "C5'" "H5'2" SING N N 10 C38 "C4'" "O4'" SING N N 11 C38 "C4'" "C3'" SING N N 12 C38 "C4'" "H4'" SING N N 13 C38 "O4'" "C1'" SING N N 14 C38 "C3'" "O3'" SING N N 15 C38 "C3'" "C2'" SING N N 16 C38 "C3'" "H3'" SING N N 17 C38 "O3'" HA SING N N 18 C38 "C2'" "C1'" SING N N 19 C38 "C2'" "H2'1" SING N N 20 C38 "C2'" "H2'2" SING N N 21 C38 "C1'" N1 SING N N 22 C38 "C1'" "H1'" SING N N 23 C38 N1 C2 SING N N 24 C38 N1 C6 SING N N 25 C38 C2 O2 DOUB N N 26 C38 C2 N3 SING N N 27 C38 N3 C4 DOUB N N 28 C38 C4 N4 SING N N 29 C38 C4 C5 SING N N 30 C38 N4 H4N1 SING N N 31 C38 N4 H4N2 SING N N 32 C38 C5 C6 DOUB N N 33 C38 C5 I SING N N 34 C38 C6 H6 SING N N 35 # 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 C38 SMILES ACDLabs 10.04 "IC=1C(=NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O)N" C38 SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1I)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" C38 SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1I)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" C38 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)I)COP(=O)(O)O)O" C38 SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=NC2=O)N)I)COP(=O)(O)O)O" C38 InChI InChI 1.03 "InChI=1S/C9H13IN3O7P/c10-4-2-13(9(15)12-8(4)11)7-1-5(14)6(20-7)3-19-21(16,17)18/h2,5-7,14H,1,3H2,(H2,11,12,15)(H2,16,17,18)/t5-,6+,7+/m0/s1" C38 InChIKey InChI 1.03 JYCZFDPCUJKMMG-RRKCRQDMSA-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 C38 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5-iodocytidine 5'-(dihydrogen phosphate) ; C38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-5-iodo-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 C38 "Create component" 1997-03-12 RCSB C38 "Modify descriptor" 2011-06-04 RCSB #