data_5CM # _chem_comp.id 5CM _chem_comp.name "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 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 1999-07-08 _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 321.224 _chem_comp.one_letter_code C _chem_comp.three_letter_code 5CM _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 1BSU _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 5CM N1 N1 N 0 1 N N N -6.764 4.376 -2.686 -0.347 -0.407 2.286 N1 5CM 1 5CM C2 C2 C 0 1 N N N -6.371 3.063 -2.997 0.114 0.856 2.277 C2 5CM 2 5CM N3 N3 N 0 1 N N N -6.060 2.741 -4.275 0.826 1.335 3.296 N3 5CM 3 5CM C4 C4 C 0 1 N N N -6.146 3.660 -5.224 1.094 0.576 4.351 C4 5CM 4 5CM C5 C5 C 0 1 N N N -6.585 5.001 -4.944 0.629 -0.754 4.388 C5 5CM 5 5CM C5A C5A C 0 1 N N N -6.653 5.992 -6.052 0.927 -1.635 5.574 C5A 5CM 6 5CM C6 C6 C 0 1 N N N -6.901 5.303 -3.678 -0.093 -1.226 3.345 C6 5CM 7 5CM O2 O2 O 0 1 N N N -6.317 2.232 -2.087 -0.124 1.575 1.321 O2 5CM 8 5CM N4 N4 N 0 1 N N N -5.804 3.305 -6.460 1.831 1.081 5.397 N4 5CM 9 5CM "C1'" C1* C 0 1 N N R -6.948 4.750 -1.277 -1.128 -0.905 1.151 "C1'" 5CM 10 5CM "C2'" C2* C 0 1 N N N -5.910 5.808 -1.036 -2.394 -0.046 0.969 "C2'" 5CM 11 5CM "C3'" C3* C 0 1 N N S -6.658 7.044 -0.587 -2.274 0.504 -0.472 "C3'" 5CM 12 5CM "C4'" C4* C 0 1 N N R -8.122 6.650 -0.467 -1.288 -0.498 -1.122 "C4'" 5CM 13 5CM "O4'" O4* O 0 1 N N N -8.222 5.359 -1.127 -0.358 -0.798 -0.057 "O4'" 5CM 14 5CM "O3'" O3* O 0 1 N N N -5.995 7.611 0.520 -3.540 0.478 -1.135 "O3'" 5CM 15 5CM "C5'" C5* C 0 1 N N N -8.971 7.591 -1.284 -0.566 0.146 -2.307 "C5'" 5CM 16 5CM "O5'" O5* O 0 1 N N N -8.233 8.001 -2.450 0.336 -0.797 -2.887 "O5'" 5CM 17 5CM P P P 0 1 N N N -8.823 9.079 -3.449 1.057 -0.055 -4.120 P 5CM 18 5CM OP1 O1P O 0 1 N N N -7.912 9.098 -4.649 1.787 1.131 -3.623 OP1 5CM 19 5CM OP2 O2P O 0 1 N N N -9.120 10.362 -2.728 2.093 -1.067 -4.824 OP2 5CM 20 5CM OP3 O3P O 0 1 N Y N -10.237 8.438 -3.818 -0.052 0.406 -5.191 OP3 5CM 21 5CM H5A1 1H5A H 0 0 N N N -6.993 7.031 -5.835 1.516 -1.077 6.302 H5A1 5CM 22 5CM H5A2 2H5A H 0 0 N N N -5.656 6.039 -6.550 -0.008 -1.956 6.032 H5A2 5CM 23 5CM H5A3 3H5A H 0 0 N N N -7.286 5.572 -6.867 1.489 -2.509 5.245 H5A3 5CM 24 5CM H6 H6 H 0 1 N N N -7.274 6.316 -3.452 -0.463 -2.240 3.352 H6 5CM 25 5CM HN41 1HN4 H 0 0 N N N -5.870 4.013 -7.191 2.155 1.995 5.365 HN41 5CM 26 5CM HN42 2HN4 H 0 0 N N N -6.344 2.484 -6.736 2.025 0.524 6.167 HN42 5CM 27 5CM "H1'" H1* H 0 1 N N N -6.867 3.876 -0.588 -1.408 -1.945 1.322 "H1'" 5CM 28 5CM "H2'" 1H2* H 0 1 N N N -5.112 5.491 -0.324 -3.290 -0.659 1.069 "H2'" 5CM 29 5CM "H2''" 2H2* H 0 0 N N N -5.247 5.986 -1.915 -2.408 0.771 1.690 "H2''" 5CM 30 5CM "H3'" H3* H 0 1 N N N -6.660 7.896 -1.305 -1.859 1.512 -0.470 "H3'" 5CM 31 5CM "H4'" H4* H 0 1 N N N -8.450 6.655 0.598 -1.810 -1.400 -1.438 "H4'" 5CM 32 5CM "HO3'" *HO3 H 0 0 N Y N -6.464 8.387 0.801 -4.133 1.051 -0.629 "HO3'" 5CM 33 5CM "H5'" 1H5* H 0 1 N N N -9.962 7.150 -1.543 -1.297 0.456 -3.053 "H5'" 5CM 34 5CM "H5''" 2H5* H 0 0 N N N -9.336 8.459 -0.686 -0.008 1.017 -1.962 "H5''" 5CM 35 5CM HOP2 2HOP H 0 0 N N N -9.473 11.008 -3.327 2.502 -0.585 -5.555 HOP2 5CM 36 5CM HOP3 3HOP H 0 0 N N N -10.590 9.084 -4.417 -0.504 -0.394 -5.489 HOP3 5CM 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 5CM N1 C2 SING N N 1 5CM N1 C6 SING N N 2 5CM N1 "C1'" SING N N 3 5CM C2 N3 SING N N 4 5CM C2 O2 DOUB N N 5 5CM N3 C4 DOUB N N 6 5CM C4 C5 SING N N 7 5CM C4 N4 SING N N 8 5CM C5 C5A SING N N 9 5CM C5 C6 DOUB N N 10 5CM C5A H5A1 SING N N 11 5CM C5A H5A2 SING N N 12 5CM C5A H5A3 SING N N 13 5CM C6 H6 SING N N 14 5CM N4 HN41 SING N N 15 5CM N4 HN42 SING N N 16 5CM "C1'" "C2'" SING N N 17 5CM "C1'" "O4'" SING N N 18 5CM "C1'" "H1'" SING N N 19 5CM "C2'" "C3'" SING N N 20 5CM "C2'" "H2'" SING N N 21 5CM "C2'" "H2''" SING N N 22 5CM "C3'" "C4'" SING N N 23 5CM "C3'" "O3'" SING N N 24 5CM "C3'" "H3'" SING N N 25 5CM "C4'" "O4'" SING N N 26 5CM "C4'" "C5'" SING N N 27 5CM "C4'" "H4'" SING N N 28 5CM "O3'" "HO3'" SING N N 29 5CM "C5'" "O5'" SING N N 30 5CM "C5'" "H5'" SING N N 31 5CM "C5'" "H5''" SING N N 32 5CM "O5'" P SING N N 33 5CM P OP1 DOUB N N 34 5CM P OP2 SING N N 35 5CM P OP3 SING N N 36 5CM OP2 HOP2 SING N N 37 5CM OP3 HOP3 SING N N 38 # 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 5CM SMILES ACDLabs 10.04 "O=C1N=C(N)C(=CN1C2OC(C(O)C2)COP(=O)(O)O)C" 5CM SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1N" 5CM SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1N" 5CM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 5CM SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O" 5CM InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(20-8)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" 5CM InChIKey InChI 1.03 RGDVNLHBCKWZDA-XLPZGREQSA-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 5CM "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5-methylcytidine 5'-(dihydrogen phosphate) ; 5CM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-5-methyl-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 5CM "Create component" 1999-07-08 RCSB 5CM "Modify descriptor" 2011-06-04 RCSB #