data_CSM # _chem_comp.id CSM _chem_comp.name "1-{2,5-anhydro-6-O-methyl-4-[(phosphonooxy)methyl]-alpha-L-mannofuranosyl}pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-01-11 _chem_comp.pdbx_modified_date 2012-06-15 _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 380.245 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CSM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3UKE _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 CSM P P P 0 1 N N N 4.480 6.337 -7.781 -3.714 -2.002 0.187 P CSM 1 CSM N1 N1 N 0 1 N N N 0.118 3.667 -5.751 2.842 -0.126 0.386 N1 CSM 2 CSM C2 C2 C 0 1 N N N -0.950 2.909 -5.501 4.031 0.369 0.774 C2 CSM 3 CSM O2 O2 O 0 1 N N N -1.683 3.157 -4.377 4.068 1.385 1.440 O2 CSM 4 CSM N3 N3 N 0 1 N N N -1.309 1.905 -6.331 5.180 -0.245 0.436 N3 CSM 5 CSM C4 C4 C 0 1 N N N -0.571 1.666 -7.428 5.157 -1.373 -0.301 C4 CSM 6 CSM O4 O4 O 0 1 N N N -0.932 0.654 -8.231 6.196 -1.930 -0.607 O4 CSM 7 CSM C5 C5 C 0 1 N N N 0.559 2.440 -7.718 3.912 -1.906 -0.717 C5 CSM 8 CSM C6 C6 C 0 1 N N N 0.894 3.451 -6.824 2.775 -1.272 -0.359 C6 CSM 9 CSM "C1'" "C1'" C 0 1 N N R 0.374 4.804 -4.844 1.608 0.564 0.769 "C1'" CSM 10 CSM "C2'" "C2'" C 0 1 N N R 1.223 4.479 -3.632 1.286 1.701 -0.251 "C2'" CSM 11 CSM O2A O2A O 0 1 N N N 1.122 5.643 -2.772 0.214 2.450 0.390 O2A CSM 12 CSM "C3'" "C3'" C 0 1 N N S 2.587 4.635 -4.252 0.482 0.864 -1.310 "C3'" CSM 13 CSM "O3'" "O3'" O 0 1 N N N 3.608 4.679 -3.237 -0.212 1.688 -2.248 "O3'" CSM 14 CSM "C4'" "C4'" C 0 1 N N R 2.256 6.053 -4.721 -0.474 0.247 -0.226 "C4'" CSM 15 CSM "O4'" "O4'" O 0 1 N N N 1.106 5.844 -5.535 0.487 -0.340 0.698 "O4'" CSM 16 CSM "C5'" "C5'" C 0 1 N N N 3.374 6.738 -5.478 -1.592 -0.664 -0.734 "C5'" CSM 17 CSM "O5'" "O5'" O 0 1 N N N 3.866 5.795 -6.429 -2.432 -1.043 0.358 "O5'" CSM 18 CSM "C6'" "C6'" C 0 1 N N S 1.698 6.758 -3.489 -0.919 1.563 0.486 "C6'" CSM 19 CSM "C7'" "C7'" C 0 1 N N N 2.763 7.521 -2.696 -2.128 2.169 -0.228 "C7'" CSM 20 CSM "O8'" "O8'" O 0 1 N N N 2.211 7.901 -1.436 -2.593 3.306 0.503 "O8'" CSM 21 CSM "C9'" "C9'" C 0 1 N N N 1.380 9.049 -1.507 -3.727 3.950 -0.083 "C9'" CSM 22 CSM OP1 OP1 O 0 1 N N N 5.513 7.393 -7.432 -4.817 -1.266 -0.727 OP1 CSM 23 CSM OP2 OP2 O 0 1 N N N 4.800 5.129 -8.616 -3.301 -3.267 -0.460 OP2 CSM 24 CSM OP3 OP3 O 0 1 N Y N 3.389 7.221 -8.529 -4.343 -2.319 1.635 OP3 CSM 25 CSM H5 H5 H 0 1 N N N 1.149 2.258 -8.604 3.873 -2.808 -1.308 H5 CSM 26 CSM H6 H6 H 0 1 N N N 1.772 4.057 -6.992 1.816 -1.664 -0.667 H6 CSM 27 CSM "H1'" "H1'" H 0 1 N N N -0.589 5.206 -4.496 1.702 0.974 1.774 "H1'" CSM 28 CSM "H2'" "H2'" H 0 1 N N N 1.024 3.503 -3.165 2.134 2.284 -0.611 "H2'" CSM 29 CSM "H3'" "H3'" H 0 1 N N N 2.782 3.935 -5.078 1.098 0.111 -1.803 "H3'" CSM 30 CSM "HO3'" "HO3'" H 0 0 N Y N 4.459 4.777 -3.647 0.366 2.253 -2.779 "HO3'" CSM 31 CSM "H5'" "H5'" H 0 1 N N N 2.991 7.631 -5.994 -2.184 -0.133 -1.480 "H5'" CSM 32 CSM "H5'A" "H5'A" H 0 0 N N N 4.177 7.031 -4.785 -1.158 -1.557 -1.184 "H5'A" CSM 33 CSM "H6'" "H6'" H 0 1 N N N 0.910 7.459 -3.800 -1.156 1.365 1.531 "H6'" CSM 34 CSM "H7'" "H7'" H 0 1 N N N 3.639 6.875 -2.537 -1.840 2.476 -1.234 "H7'" CSM 35 CSM "H7'A" "H7'A" H 0 0 N N N 3.066 8.420 -3.253 -2.924 1.426 -0.289 "H7'A" CSM 36 CSM "H9'" "H9'" H 0 1 N N N 0.991 9.283 -0.505 -4.017 4.802 0.531 "H9'" CSM 37 CSM "H9'A" "H9'A" H 0 0 N N N 1.965 9.902 -1.882 -3.472 4.294 -1.085 "H9'A" CSM 38 CSM "H9'B" "H9'B" H 0 0 N N N 0.540 8.852 -2.189 -4.555 3.244 -0.141 "H9'B" CSM 39 CSM HOP1 HOP1 H 0 0 N N N 6.349 7.159 -7.818 -5.134 -0.428 -0.363 HOP1 CSM 40 CSM HOP3 HOP3 H 0 0 N Y N 3.158 6.809 -9.353 -5.121 -2.894 1.608 HOP3 CSM 41 CSM HN3 HN3 H 0 1 N N N -2.114 1.347 -6.131 6.029 0.126 0.725 HN3 CSM 42 # 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 CSM OP2 P DOUB N N 1 CSM OP3 P SING N N 2 CSM P OP1 SING N N 3 CSM P "O5'" SING N N 4 CSM C6 N1 SING N N 5 CSM N1 C2 SING N N 6 CSM N1 "C1'" SING N N 7 CSM N3 C2 SING N N 8 CSM C2 O2 DOUB N N 9 CSM C4 N3 SING N N 10 CSM O4 C4 DOUB N N 11 CSM C5 C4 SING N N 12 CSM C5 C6 DOUB N N 13 CSM C5 H5 SING N N 14 CSM C6 H6 SING N N 15 CSM "O4'" "C1'" SING N N 16 CSM "C1'" "C2'" SING N N 17 CSM "C1'" "H1'" SING N N 18 CSM "C3'" "C2'" SING N N 19 CSM "C2'" O2A SING N N 20 CSM "C2'" "H2'" SING N N 21 CSM "C6'" O2A SING N N 22 CSM "C4'" "C3'" SING N N 23 CSM "C3'" "O3'" SING N N 24 CSM "C3'" "H3'" SING N N 25 CSM "O3'" "HO3'" SING N N 26 CSM "O4'" "C4'" SING N N 27 CSM "C5'" "C4'" SING N N 28 CSM "C4'" "C6'" SING N N 29 CSM "O5'" "C5'" SING N N 30 CSM "C5'" "H5'" SING N N 31 CSM "C5'" "H5'A" SING N N 32 CSM "C6'" "C7'" SING N N 33 CSM "C6'" "H6'" SING N N 34 CSM "C7'" "O8'" SING N N 35 CSM "C7'" "H7'" SING N N 36 CSM "C7'" "H7'A" SING N N 37 CSM "C9'" "O8'" SING N N 38 CSM "C9'" "H9'" SING N N 39 CSM "C9'" "H9'A" SING N N 40 CSM "C9'" "H9'B" SING N N 41 CSM OP1 HOP1 SING N N 42 CSM OP3 HOP3 SING N N 43 CSM N3 HN3 SING N N 44 # 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 CSM SMILES ACDLabs 12.01 "O=P(O)(O)OCC32OC(N1C(=O)NC(=O)C=C1)C(OC2COC)C3O" CSM InChI InChI 1.03 "InChI=1S/C12H17N2O10P/c1-21-4-6-12(5-22-25(18,19)20)9(16)8(23-6)10(24-12)14-3-2-7(15)13-11(14)17/h2-3,6,8-10,16H,4-5H2,1H3,(H,13,15,17)(H2,18,19,20)/t6-,8+,9-,10+,12-/m0/s1" CSM InChIKey InChI 1.03 CCBFKLZCTXQEKB-FIRPKLOMSA-N CSM SMILES_CANONICAL CACTVS 3.370 "COC[C@@H]1O[C@@H]2[C@H](O)[C@@]1(CO[P](O)(O)=O)O[C@H]2N3C=CC(=O)NC3=O" CSM SMILES CACTVS 3.370 "COC[CH]1O[CH]2[CH](O)[C]1(CO[P](O)(O)=O)O[CH]2N3C=CC(=O)NC3=O" CSM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "COC[C@H]1[C@]2([C@H]([C@@H](O1)[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" CSM SMILES "OpenEye OEToolkits" 1.7.6 "COCC1C2(C(C(O1)C(O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" # 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 CSM "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2,5-anhydro-6-O-methyl-4-[(phosphonooxy)methyl]-alpha-L-mannofuranosyl}pyrimidine-2,4(1H,3H)-dione" CSM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1R,3S,4R,6R,7S)-6-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-(methoxymethyl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-4-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 CSM "Create component" 2012-01-11 RCSB #