data_SMP # _chem_comp.id SMP _chem_comp.name "2'-DEOXY-ADENOSINE-5'-SP-MONOMETHYLPHOSPHONATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O5 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-10-09 _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 329.249 _chem_comp.one_letter_code A _chem_comp.three_letter_code SMP _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 SMP P P P 0 1 N N R -5.403 -6.827 6.538 1.656 -1.229 -4.986 P SMP 1 SMP CMP CMP C 0 1 N N N -6.609 -8.104 6.349 1.011 -2.866 -5.265 CMP SMP 2 SMP OP1 O1P O 0 1 N N N -4.990 -6.969 7.947 2.664 -0.795 -6.011 OP1 SMP 3 SMP "O5'" O5* O 0 1 N N N -5.890 -5.321 6.327 2.211 -1.232 -3.468 "O5'" SMP 4 SMP "C5'" C5* C 0 1 N N N -5.168 -4.259 6.876 1.348 -1.500 -2.377 "C5'" SMP 5 SMP "C4'" C4* C 0 1 N N R -5.763 -2.911 6.523 2.156 -1.432 -1.088 "C4'" SMP 6 SMP "O4'" O4* O 0 1 N N N -5.543 -2.629 5.165 2.678 -0.093 -0.958 "O4'" SMP 7 SMP "C1'" C1* C 0 1 N N R -6.602 -1.841 4.705 2.101 0.516 0.211 "C1'" SMP 8 SMP N9 N9 N 0 1 Y N N -6.707 -1.931 3.247 1.818 1.923 -0.049 N9 SMP 9 SMP C8 C8 C 0 1 Y N N -6.960 -3.022 2.486 1.432 2.463 -1.249 C8 SMP 10 SMP N7 N7 N 0 1 Y N N -7.133 -2.752 1.224 1.250 3.765 -1.175 N7 SMP 11 SMP C5 C5 C 0 1 Y N N -6.951 -1.382 1.157 1.530 4.086 0.130 C5 SMP 12 SMP C6 C6 C 0 1 Y N N -6.986 -0.454 0.094 1.519 5.292 0.822 C6 SMP 13 SMP N6 N6 N 0 1 N N N -7.202 -0.771 -1.171 1.171 6.489 0.173 N6 SMP 14 SMP N1 N1 N 0 1 Y N N -6.795 0.840 0.359 1.849 5.300 2.136 N1 SMP 15 SMP C2 C2 C 0 1 Y N N -6.575 1.206 1.611 2.176 4.115 2.707 C2 SMP 16 SMP N3 N3 N 0 1 Y N N -6.503 0.451 2.697 2.223 2.888 2.144 N3 SMP 17 SMP C4 C4 C 0 1 Y N N -6.703 -0.861 2.397 1.886 2.954 0.847 C4 SMP 18 SMP "C3'" C3* C 0 1 N N S -7.263 -2.718 6.786 1.309 -1.697 0.152 "C3'" SMP 19 SMP "C2'" C2* C 0 1 N N N -7.783 -2.489 5.382 0.878 -0.312 0.578 "C2'" SMP 20 SMP "O3'" O3* O 0 1 N N N -7.348 -1.612 7.656 2.127 -2.250 1.180 "O3'" SMP 21 SMP OP3 O3P O 0 1 N Y N ? ? ? 0.334 -0.300 -4.927 OP3 SMP 22 SMP HMP1 1HMP H 0 0 N N N -7.170 -7.943 5.417 1.738 -3.616 -4.945 HMP1 SMP 23 SMP HMP2 2HMP H 0 0 N N N -7.302 -8.083 7.203 0.087 -3.006 -4.699 HMP2 SMP 24 SMP HMP3 3HMP H 0 0 N N N -6.106 -9.081 6.310 0.799 -3.010 -6.328 HMP3 SMP 25 SMP "H5'" 1H5* H 0 1 N N N -4.149 -4.296 6.463 0.551 -0.756 -2.359 "H5'" SMP 26 SMP "H5''" 2H5* H 0 0 N N N -5.170 -4.365 7.971 0.917 -2.495 -2.497 "H5''" SMP 27 SMP "H4'" H4* H 0 1 N N N -5.242 -2.226 7.208 3.008 -2.117 -1.157 "H4'" SMP 28 SMP "H1'" H1* H 0 1 N N N -6.503 -0.768 4.926 2.853 0.503 1.007 "H1'" SMP 29 SMP H8 H8 H 0 1 N N N -7.013 -4.023 2.888 1.301 1.859 -2.137 H8 SMP 30 SMP H61 1H6 H 0 1 N N N -6.825 -0.058 -1.762 0.205 6.745 0.096 H61 SMP 31 SMP H62 2H6 H 0 1 N N N -8.186 -0.851 -1.332 1.883 7.025 -0.286 H62 SMP 32 SMP H2 H2 H 0 1 N N N -6.435 2.265 1.769 2.435 4.159 3.759 H2 SMP 33 SMP "H3'" H3* H 0 1 N N N -7.835 -3.526 7.266 0.475 -2.383 -0.018 "H3'" SMP 34 SMP "H2'" 1H2* H 0 1 N N N -8.122 -3.410 4.885 0.008 0.008 -0.009 "H2'" SMP 35 SMP "H2''" 2H2* H 0 0 N N N -8.670 -1.839 5.373 0.635 -0.225 1.641 "H2''" SMP 36 SMP "HO3'" H3T H 0 0 N Y N -8.260 -1.432 7.852 2.928 -1.706 1.218 "HO3'" SMP 37 SMP HOP3 3HOP H 0 0 N N N 0.649 0.687 0.102 0.440 0.671 -4.846 HOP3 SMP 38 # 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 SMP P CMP SING N N 1 SMP P OP1 DOUB N N 2 SMP P "O5'" SING N N 3 SMP P OP3 SING N N 4 SMP CMP HMP1 SING N N 5 SMP CMP HMP2 SING N N 6 SMP CMP HMP3 SING N N 7 SMP "O5'" "C5'" SING N N 8 SMP "C5'" "C4'" SING N N 9 SMP "C5'" "H5'" SING N N 10 SMP "C5'" "H5''" SING N N 11 SMP "C4'" "O4'" SING N N 12 SMP "C4'" "C3'" SING N N 13 SMP "C4'" "H4'" SING N N 14 SMP "O4'" "C1'" SING N N 15 SMP "C1'" N9 SING N N 16 SMP "C1'" "C2'" SING N N 17 SMP "C1'" "H1'" SING N N 18 SMP N9 C8 SING Y N 19 SMP N9 C4 SING Y N 20 SMP C8 N7 DOUB Y N 21 SMP C8 H8 SING N N 22 SMP N7 C5 SING Y N 23 SMP C5 C6 DOUB Y N 24 SMP C5 C4 SING Y N 25 SMP C6 N6 SING N N 26 SMP C6 N1 SING Y N 27 SMP N6 H61 SING N N 28 SMP N6 H62 SING N N 29 SMP N1 C2 DOUB Y N 30 SMP C2 N3 SING Y N 31 SMP C2 H2 SING N N 32 SMP N3 C4 DOUB Y N 33 SMP "C3'" "C2'" SING N N 34 SMP "C3'" "O3'" SING N N 35 SMP "C3'" "H3'" SING N N 36 SMP "C2'" "H2'" SING N N 37 SMP "C2'" "H2''" SING N N 38 SMP "O3'" "HO3'" SING N N 39 SMP OP3 HOP3 SING N N 40 # 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 SMP SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n2cnc1c(ncnc12)N)CC3O)C" SMP SMILES_CANONICAL CACTVS 3.341 "C[P@](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3c(N)ncnc23" SMP SMILES CACTVS 3.341 "C[P](O)(=O)OC[CH]1O[CH](C[CH]1O)n2cnc3c(N)ncnc23" SMP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[P@@](=O)(O)OC[C@@H]1[C@H](C[C@@H](O1)n2cnc3c2ncnc3N)O" SMP SMILES "OpenEye OEToolkits" 1.5.0 "CP(=O)(O)OCC1C(CC(O1)n2cnc3c2ncnc3N)O" SMP InChI InChI 1.03 "InChI=1S/C11H16N5O5P/c1-22(18,19)20-3-7-6(17)2-8(21-7)16-5-15-9-10(12)13-4-14-11(9)16/h4-8,17H,2-3H2,1H3,(H,18,19)(H2,12,13,14)/t6-,7+,8+/m0/s1" SMP InChIKey InChI 1.03 YNCYIAAXFUCITC-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 SMP "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-[(R)-hydroxy(methyl)phosphoryl]adenosine" SMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-methyl-phosphinic 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 SMP "Create component" 2001-10-09 RCSB SMP "Modify descriptor" 2011-06-04 RCSB #