data_M5M # _chem_comp.id M5M _chem_comp.name "2'-(N-ACETAMIDE)-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N4 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 2005-03-17 _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 364.248 _chem_comp.one_letter_code C _chem_comp.three_letter_code M5M _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 1YY0 _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 M5M P P P 0 1 N N N -1.561 35.026 57.421 1.304 -3.478 3.683 P M5M 1 M5M "N2'" N2* N 0 1 N N N 4.845 33.413 58.668 0.180 2.821 0.827 "N2'" M5M 2 M5M "C6'" C6* C 0 1 N N N 6.050 32.867 58.808 1.177 3.777 0.842 "C6'" M5M 3 M5M "C7'" C7* C 0 1 N N N 7.181 33.659 58.213 0.852 5.006 0.059 "C7'" M5M 4 M5M "O8'" O8* O 0 1 N N N 6.242 31.806 59.407 2.255 3.697 1.421 "O8'" M5M 5 M5M OP1 O1P O 0 1 N N N -1.560 36.032 56.333 0.943 -4.335 4.861 OP1 M5M 6 M5M OP2 O2P O 0 1 N N N -2.584 33.952 57.423 2.679 -2.641 3.832 OP2 M5M 7 M5M "O5'" O5* O 0 1 N N N -0.093 34.403 57.537 0.208 -2.352 3.295 "O5'" M5M 8 M5M "C5'" C5* C 0 1 N N N 1.050 35.262 57.542 0.474 -1.502 2.192 "C5'" M5M 9 M5M "C4'" C4* C 0 1 N N R 2.269 34.558 58.107 -0.690 -0.534 2.024 "C4'" M5M 10 M5M "O4'" O4* O 0 1 N N N 1.957 34.044 59.427 -0.776 0.278 3.212 "O4'" M5M 11 M5M "C1'" C1* C 0 1 N N R 2.710 32.867 59.668 -0.283 1.598 2.925 "C1'" M5M 12 M5M N1 N1 N 0 1 N N N 1.773 31.758 59.865 0.699 1.953 3.911 N1 M5M 13 M5M C6 C6 C 0 1 N N N 0.449 31.892 59.561 1.502 0.955 4.436 C6 M5M 14 M5M C2 C2 C 0 1 N N N 2.262 30.554 60.360 0.864 3.288 4.354 C2 M5M 15 M5M O2 O2 O 0 1 N N N 3.463 30.475 60.649 0.165 4.198 3.905 O2 M5M 16 M5M N3 N3 N 0 1 N N N 1.424 29.511 60.515 1.831 3.558 5.307 N3 M5M 17 M5M C4 C4 C 0 1 N N N 0.138 29.643 60.198 2.582 2.606 5.795 C4 M5M 18 M5M N4 N4 N 0 1 N N N -0.654 28.579 60.341 3.537 2.895 6.742 N4 M5M 19 M5M C5 C5 C 0 1 N N N -0.396 30.869 59.712 2.437 1.194 5.353 C5 M5M 20 M5M "C2'" C2* C 0 1 N N R 3.622 32.657 58.460 0.288 1.564 1.513 "C2'" M5M 21 M5M "C3'" C3* C 0 1 N N S 2.819 33.347 57.365 -0.501 0.439 0.868 "C3'" M5M 22 M5M "O3'" O3* O 0 1 N N N 3.680 33.723 56.292 -1.784 0.893 0.436 "O3'" M5M 23 M5M OP3 O3P O 0 1 N Y N ? ? ? 1.504 -4.279 2.292 OP3 M5M 24 M5M "HN'2" 2HN* H 0 0 N N N 4.859 34.431 58.721 -0.669 3.015 0.305 "HN'2" M5M 25 M5M "H7'1" 1H7* H 0 0 N N N 8.191 33.201 58.330 0.866 5.916 0.680 "H7'1" M5M 26 M5M "H7'2" 2H7* H 0 0 N N N 6.977 33.871 57.137 1.578 5.194 -0.749 "H7'2" M5M 27 M5M "H7'3" 3H7* H 0 0 N N N 7.179 34.697 58.620 -0.134 5.005 -0.432 "H7'3" M5M 28 M5M HOP2 2HOP H 0 0 N N N -2.584 33.307 58.120 3.488 -3.107 4.133 HOP2 M5M 29 M5M "H5'" 1H5* H 0 1 N N N 1.252 35.678 56.527 1.399 -0.952 2.382 "H5'" M5M 30 M5M "H5''" 2H5* H 0 0 N N N 0.842 36.215 58.081 0.594 -2.111 1.294 "H5''" M5M 31 M5M "H4'" H4* H 0 1 N N N 3.039 35.361 58.048 -1.623 -1.101 1.939 "H4'" M5M 32 M5M "H1'" H1* H 0 1 N N N 3.344 32.938 60.581 -1.119 2.298 3.025 "H1'" M5M 33 M5M H6 H6 H 0 1 N N N 0.052 32.849 59.184 1.329 -0.047 4.059 H6 M5M 34 M5M HN41 1HN4 H 0 0 N N N -1.639 28.680 60.098 4.473 2.623 6.558 HN41 M5M 35 M5M HN42 2HN4 H 0 0 N N N -0.579 28.232 61.297 3.249 3.364 7.567 HN42 M5M 36 M5M H5 H5 H 0 1 N N N -1.457 31.025 59.454 3.068 0.420 5.769 H5 M5M 37 M5M "H2'" H2* H 0 1 N N N 3.891 31.594 58.254 1.352 1.300 1.534 "H2'" M5M 38 M5M "H3'" H3* H 0 1 N N N 2.023 32.721 56.896 0.000 -0.002 0.001 "H3'" M5M 39 M5M "HO3'" H3T H 0 0 N Y N 4.023 32.967 55.829 -1.742 1.003 -0.531 "HO3'" M5M 40 M5M HOP3 3HOP H 0 0 N N N 0.000 -0.645 0.697 2.064 -5.085 2.285 HOP3 M5M 41 # 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 M5M P OP1 DOUB N N 1 M5M P OP2 SING N N 2 M5M P "O5'" SING N N 3 M5M P OP3 SING N N 4 M5M "N2'" "C6'" SING N N 5 M5M "N2'" "C2'" SING N N 6 M5M "N2'" "HN'2" SING N N 7 M5M "C6'" "C7'" SING N N 8 M5M "C6'" "O8'" DOUB N N 9 M5M "C7'" "H7'1" SING N N 10 M5M "C7'" "H7'2" SING N N 11 M5M "C7'" "H7'3" SING N N 12 M5M OP2 HOP2 SING N N 13 M5M "O5'" "C5'" SING N N 14 M5M "C5'" "C4'" SING N N 15 M5M "C5'" "H5'" SING N N 16 M5M "C5'" "H5''" SING N N 17 M5M "C4'" "O4'" SING N N 18 M5M "C4'" "C3'" SING N N 19 M5M "C4'" "H4'" SING N N 20 M5M "O4'" "C1'" SING N N 21 M5M "C1'" N1 SING N N 22 M5M "C1'" "C2'" SING N N 23 M5M "C1'" "H1'" SING N N 24 M5M N1 C6 SING N N 25 M5M N1 C2 SING N N 26 M5M C6 C5 DOUB N N 27 M5M C6 H6 SING N N 28 M5M C2 O2 DOUB N N 29 M5M C2 N3 SING N N 30 M5M N3 C4 DOUB N N 31 M5M C4 N4 SING N N 32 M5M C4 C5 SING N N 33 M5M N4 HN41 SING N N 34 M5M N4 HN42 SING N N 35 M5M C5 H5 SING N N 36 M5M "C2'" "C3'" SING N N 37 M5M "C2'" "H2'" SING N N 38 M5M "C3'" "O3'" SING N N 39 M5M "C3'" "H3'" SING N N 40 M5M "O3'" "HO3'" SING N N 41 M5M OP3 HOP3 SING N N 42 # 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 M5M SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2NC(=O)C)COP(=O)(O)O" M5M SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N" M5M SMILES CACTVS 3.341 "CC(=O)N[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" M5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" M5M SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" M5M InChI InChI 1.03 "InChI=1S/C11H17N4O8P/c1-5(16)13-8-9(17)6(4-22-24(19,20)21)23-10(8)15-3-2-7(12)14-11(15)18/h2-3,6,8-10,17H,4H2,1H3,(H,13,16)(H2,12,14,18)(H2,19,20,21)/t6-,8-,9-,10-/m1/s1" M5M InChIKey InChI 1.03 WPJHNTZXIXFENS-PEBGCTIMSA-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 M5M "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-(acetylamino)-2'-deoxycytidine 5'-(dihydrogen phosphate) ; M5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-4-acetamido-5-(4-amino-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 M5M "Create component" 2005-03-17 RCSB M5M "Modify descriptor" 2011-06-04 RCSB #