data_LKC # _chem_comp.id LKC _chem_comp.name "4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N3 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-06-27 _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 269.254 _chem_comp.one_letter_code N _chem_comp.three_letter_code LKC _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 1H0Q _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 LKC N1 N1 N 0 1 N N N -7.188 -9.451 1.189 -0.418 -0.393 0.957 N1 LKC 1 LKC C2 C2 C 0 1 N N N -5.874 -9.822 1.509 -1.336 -0.443 1.940 C2 LKC 2 LKC N3 N3 N 0 1 N N N -4.915 -9.757 0.542 -1.000 -0.210 3.207 N3 LKC 3 LKC C4 C4 C 0 1 N N N -5.203 -9.332 -0.696 0.253 0.073 3.534 C4 LKC 4 LKC C5 C5 C 0 1 N N N -6.543 -8.915 -1.044 1.238 0.139 2.528 C5 LKC 5 LKC C6 C6 C 0 1 N N N -7.492 -8.991 -0.075 0.881 -0.100 1.244 C6 LKC 6 LKC O2 O2 O 0 1 N N N -5.576 -10.206 2.640 -2.495 -0.707 1.665 O2 LKC 7 LKC N4 N4 N 0 1 N N N -4.207 -9.303 -1.587 0.588 0.313 4.847 N4 LKC 8 LKC "C1'" C1* C 0 1 N N R -8.237 -9.624 2.236 -0.817 -0.655 -0.427 "C1'" LKC 9 LKC "C2'" C2* C 0 1 N N R -8.223 -8.502 3.283 -1.350 0.651 -1.093 "C2'" LKC 10 LKC "C3'" C3* C 0 1 N N S -9.157 -7.474 2.661 0.017 1.240 -1.604 "C3'" LKC 11 LKC "C4'" C4* C 0 1 N N S -10.221 -8.558 2.553 0.429 -0.100 -2.314 "C4'" LKC 12 LKC "O4'" O4* O 0 1 N N N -9.576 -9.546 1.751 0.326 -1.046 -1.212 "O4'" LKC 13 LKC "O3'" O3* O 0 1 N N N -9.495 -6.396 3.522 -0.160 2.305 -2.540 "O3'" LKC 14 LKC "C5'" C5* C 0 1 N N N -11.549 -8.078 1.953 1.753 -0.093 -3.081 "C5'" LKC 15 LKC "O5'" O5* O 0 1 N N N -12.524 -9.100 1.995 1.969 -1.378 -3.668 "O5'" LKC 16 LKC C5A C5A C 0 1 N N N -6.890 -8.410 -2.435 2.667 0.465 2.876 C5A LKC 17 LKC "O2'" O2* O 0 1 N N N -8.929 -8.988 4.419 -1.944 0.162 -2.365 "O2'" LKC 18 LKC "C6'" C6* C 0 1 N N N -10.288 -9.062 4.005 -0.859 -0.366 -3.154 "C6'" LKC 19 LKC H6 H6 H 0 1 N N N -8.504 -8.690 -0.303 1.618 -0.060 0.456 H6 LKC 20 LKC H41 1H4 H 0 1 N N N -3.280 -9.600 -1.308 -0.093 0.274 5.536 H41 LKC 21 LKC H42 2H4 H 0 1 N N N -4.374 -8.976 -2.526 1.505 0.520 5.083 H42 LKC 22 LKC "H1'" H1* H 0 1 N N N -8.087 -10.580 2.739 -1.580 -1.433 -0.458 "H1'" LKC 23 LKC "H2'1" 1H2* H 0 0 N N N -7.226 -8.129 3.507 -1.978 1.302 -0.485 "H2'1" LKC 24 LKC "H3'" H3* H 0 1 N N N -8.824 -7.132 1.679 0.684 1.518 -0.788 "H3'" LKC 25 LKC H3T H3T H 0 1 N Y N -10.078 -5.754 3.134 -0.636 3.007 -2.077 H3T LKC 26 LKC "H5'1" 1H5* H 0 0 N N N -11.911 -7.221 2.522 1.715 0.662 -3.864 "H5'1" LKC 27 LKC "H5'2" 2H5* H 0 0 N N N -11.386 -7.771 0.918 2.568 0.134 -2.395 "H5'2" LKC 28 LKC H5T H5T H 0 1 N N N -13.337 -8.766 1.609 2.812 -1.330 -4.141 H5T LKC 29 LKC H5M1 1H5M H 0 0 N N N -6.726 -9.205 -3.163 2.752 0.624 3.951 H5M1 LKC 30 LKC H5M2 2H5M H 0 0 N N N -7.934 -8.100 -2.479 3.311 -0.362 2.580 H5M2 LKC 31 LKC H5M3 3H5M H 0 0 N N N -6.260 -7.556 -2.682 2.972 1.369 2.350 H5M3 LKC 32 LKC "H6'1" 1H6* H 0 0 N N N -10.662 -10.085 4.047 -0.800 0.152 -4.111 "H6'1" LKC 33 LKC "H6'2" 2H6* H 0 0 N N N -10.902 -8.398 4.617 -0.993 -1.436 -3.311 "H6'2" LKC 34 # 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 LKC N1 C2 SING N N 1 LKC N1 C6 SING N N 2 LKC N1 "C1'" SING N N 3 LKC C2 N3 SING N N 4 LKC C2 O2 DOUB N N 5 LKC N3 C4 DOUB N N 6 LKC C4 C5 SING N N 7 LKC C4 N4 SING N N 8 LKC C5 C6 DOUB N N 9 LKC C5 C5A SING N N 10 LKC C6 H6 SING N N 11 LKC N4 H41 SING N N 12 LKC N4 H42 SING N N 13 LKC "C1'" "C2'" SING N N 14 LKC "C1'" "O4'" SING N N 15 LKC "C1'" "H1'" SING N N 16 LKC "C2'" "C3'" SING N N 17 LKC "C2'" "O2'" SING N N 18 LKC "C2'" "H2'1" SING N N 19 LKC "C3'" "C4'" SING N N 20 LKC "C3'" "O3'" SING N N 21 LKC "C3'" "H3'" SING N N 22 LKC "C4'" "O4'" SING N N 23 LKC "C4'" "C5'" SING N N 24 LKC "C4'" "C6'" SING N N 25 LKC "O3'" H3T SING N N 26 LKC "C5'" "O5'" SING N N 27 LKC "C5'" "H5'1" SING N N 28 LKC "C5'" "H5'2" SING N N 29 LKC "O5'" H5T SING N N 30 LKC C5A H5M1 SING N N 31 LKC C5A H5M2 SING N N 32 LKC C5A H5M3 SING N N 33 LKC "O2'" "C6'" SING N N 34 LKC "C6'" "H6'1" SING N N 35 LKC "C6'" "H6'2" 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 LKC SMILES ACDLabs 10.04 "O=C1N=C(N)C(=CN1C3OC2(C(O)C3OC2)CO)C" LKC SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@@]3(CO)CO[C@@H]2[C@@H]3O)C(=O)N=C1N" LKC SMILES CACTVS 3.341 "CC1=CN([CH]2O[C]3(CO)CO[CH]2[CH]3O)C(=O)N=C1N" LKC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)CO)O" LKC SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2C3C(C(O2)(CO3)CO)O" LKC InChI InChI 1.03 "InChI=1S/C11H15N3O5/c1-5-2-14(10(17)13-8(5)12)9-6-7(16)11(3-15,19-9)4-18-6/h2,6-7,9,15-16H,3-4H2,1H3,(H2,12,13,17)/t6-,7+,9-,11+/m1/s1" LKC InChIKey InChI 1.03 NELYIRACPIJATH-SZVQBCOZSA-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 LKC "SYSTEMATIC NAME" ACDLabs 10.04 "4-amino-1-[2,5-anhydro-4-(hydroxymethyl)-alpha-L-lyxofuranosyl]-5-methylpyrimidin-2(1H)-one" LKC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(1R,4S,6R,7S)-7-hydroxy-4-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-6-yl]-5-methyl-pyrimidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site LKC "Create component" 2002-06-27 EBI LKC "Modify linking type" 2011-06-04 RCSB LKC "Modify descriptor" 2011-06-04 RCSB #