data_5IC # _chem_comp.id 5IC _chem_comp.name "5-IODO-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 I N3 O8 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-05-13 _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 449.093 _chem_comp.one_letter_code C _chem_comp.three_letter_code 5IC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _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 # 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 5IC "O2'" O2* O 0 1 N N N ? ? ? 1.026 0.515 -1.704 "O2'" 5IC 1 5IC "C2'" C2* C 0 1 N N S -0.002 14.342 38.063 0.961 0.440 -0.285 "C2'" 5IC 2 5IC "C3'" C3* C 0 1 N N S -1.307 13.736 37.557 2.168 -0.326 0.213 "C3'" 5IC 3 5IC "O3'" O3* O 0 1 N N N -1.696 12.570 38.284 1.912 -0.804 1.532 "O3'" 5IC 4 5IC "C4'" C4* C 0 1 N N R -0.993 13.317 36.118 3.261 0.741 0.292 "C4'" 5IC 5 5IC "O4'" O4* O 0 1 N N N 0.410 13.602 35.919 2.597 2.020 0.362 "O4'" 5IC 6 5IC "C1'" C1* C 0 1 N N R 1.019 13.658 37.177 1.180 1.804 0.351 "C1'" 5IC 7 5IC N1 N1 N 0 1 N N N 2.302 14.350 37.013 0.531 2.882 -0.332 N1 5IC 8 5IC C6 C6 C 0 1 N N N 2.373 15.707 36.809 1.154 3.517 -1.398 C6 5IC 9 5IC C5 C5 C 0 1 N N N 3.564 16.321 36.641 0.603 4.528 -2.075 C5 5IC 10 5IC I I I 0 1 N N N 3.652 18.357 36.148 1.535 5.445 -3.638 I 5IC 11 5IC C4 C4 C 0 1 N N N 4.748 15.504 36.723 -0.757 4.954 -1.614 C4 5IC 12 5IC N3 N3 N 0 1 N N N 4.675 14.184 36.921 -1.353 4.361 -0.609 N3 5IC 13 5IC C2 C2 C 0 1 N N N 3.473 13.582 37.055 -0.757 3.317 0.071 C2 5IC 14 5IC O2 O2 O 0 1 N N N 3.367 12.345 37.212 -1.340 2.777 1.013 O2 5IC 15 5IC N4 N4 N 0 1 N N N 5.952 16.046 36.620 -1.412 5.989 -2.245 N4 5IC 16 5IC "C5'" C5* C 0 1 N N N -1.811 14.078 35.107 4.178 0.759 -0.923 "C5'" 5IC 17 5IC "O5'" O5* O 0 1 N N N -1.727 15.474 35.378 5.140 1.786 -0.752 "O5'" 5IC 18 5IC P P P 0 1 N N N -2.283 16.517 34.319 6.242 2.013 -1.916 P 5IC 19 5IC OP1 O1P O 0 1 N N N -1.936 17.886 34.810 7.221 3.120 -1.655 OP1 5IC 20 5IC OP3 O3P O 0 1 N Y N ? ? ? 5.354 2.178 -3.258 OP3 5IC 21 5IC OP2 O2P O 0 1 N N N -3.694 16.177 34.050 6.899 0.545 -2.084 OP2 5IC 22 5IC "HO2'" 2HO* H 0 0 N N N 0.813 0.378 0.315 1.763 -0.054 -1.980 "HO2'" 5IC 23 5IC "H2'" H2* H 0 1 N N N 0.089 14.947 38.995 -0.001 0.003 -0.002 "H2'" 5IC 24 5IC "H3'" H3* H 0 1 N N N -2.141 14.469 37.662 2.451 -1.179 -0.411 "H3'" 5IC 25 5IC "HO3'" H3T H 0 0 N Y N -2.509 12.193 37.969 1.393 -0.117 1.978 "HO3'" 5IC 26 5IC "H4'" H4* H 0 1 N N N -1.239 12.239 35.973 3.870 0.634 1.195 "H4'" 5IC 27 5IC "H1'" H1* H 0 1 N N N 1.279 12.681 37.648 0.838 1.814 1.392 "H1'" 5IC 28 5IC H6 H6 H 0 1 N N N 1.454 16.317 36.780 2.137 3.128 -1.646 H6 5IC 29 5IC H41 1H4 H 0 1 N N N 6.028 16.788 37.316 -2.190 6.395 -1.785 H41 5IC 30 5IC H42 2H4 H 0 1 N N N 6.790 15.468 36.678 -1.076 6.280 -3.130 H42 5IC 31 5IC "H5'" 1H5* H 0 1 N N N -2.866 13.721 35.065 3.600 0.957 -1.828 "H5'" 5IC 32 5IC "H5''" 2H5* H 0 0 N N N -1.517 13.835 34.059 4.691 -0.199 -1.021 "H5''" 5IC 33 5IC HOP3 3HOP H 0 0 N N N -0.333 0.624 -0.634 5.805 2.397 -4.101 HOP3 5IC 34 5IC HOP2 2HOP H 0 0 N N N -4.027 16.801 33.416 7.671 0.436 -2.678 HOP2 5IC 35 # 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 5IC "O2'" "C2'" SING N N 1 5IC "O2'" "HO2'" SING N N 2 5IC "C2'" "C3'" SING N N 3 5IC "C2'" "C1'" SING N N 4 5IC "C2'" "H2'" SING N N 5 5IC "C3'" "O3'" SING N N 6 5IC "C3'" "C4'" SING N N 7 5IC "C3'" "H3'" SING N N 8 5IC "O3'" "HO3'" SING N N 9 5IC "C4'" "O4'" SING N N 10 5IC "C4'" "C5'" SING N N 11 5IC "C4'" "H4'" SING N N 12 5IC "O4'" "C1'" SING N N 13 5IC "C1'" N1 SING N N 14 5IC "C1'" "H1'" SING N N 15 5IC N1 C6 SING N N 16 5IC N1 C2 SING N N 17 5IC C6 C5 DOUB N N 18 5IC C6 H6 SING N N 19 5IC C5 I SING N N 20 5IC C5 C4 SING N N 21 5IC C4 N3 DOUB N N 22 5IC C4 N4 SING N N 23 5IC N3 C2 SING N N 24 5IC C2 O2 DOUB N N 25 5IC N4 H41 SING N N 26 5IC N4 H42 SING N N 27 5IC "C5'" "O5'" SING N N 28 5IC "C5'" "H5'" SING N N 29 5IC "C5'" "H5''" SING N N 30 5IC "O5'" P SING N N 31 5IC P OP1 DOUB N N 32 5IC P OP3 SING N N 33 5IC P OP2 SING N N 34 5IC OP3 HOP3 SING N N 35 5IC OP2 HOP2 SING N N 36 # 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 5IC SMILES ACDLabs 10.04 "IC=1C(=NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O)N" 5IC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1I)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]2O" 5IC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1I)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 5IC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)I" 5IC SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)I" 5IC InChI InChI 1.03 "InChI=1S/C9H13IN3O8P/c10-3-1-13(9(16)12-7(3)11)8-6(15)5(14)4(21-8)2-20-22(17,18)19/h1,4-6,8,14-15H,2H2,(H2,11,12,16)(H2,17,18,19)/t4-,5-,6?,8-/m1/s1" 5IC InChIKey InChI 1.03 CIUBKYYOJNFMQN-XTSMLKGCSA-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 5IC "SYSTEMATIC NAME" ACDLabs 10.04 "4-amino-5-iodo-1-(5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one" 5IC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4S,5R)-5-(4-amino-5-iodo-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-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 5IC "Create component" 2003-05-13 RCSB 5IC "Modify descriptor" 2011-06-04 RCSB #