data_C4J # _chem_comp.id C4J _chem_comp.name "(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-13 _chem_comp.pdbx_modified_date 2017-12-01 _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 439.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C4J _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 6AZ1 _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 C4J C6 C1 C 0 1 N N N 131.174 205.672 192.159 -1.326 -2.937 1.266 C6 C4J 1 C4J C5 C2 C 0 1 N N N 130.486 204.742 192.861 -0.624 -2.169 0.405 C5 C4J 2 C4J N1 N1 N 0 1 N N N 131.623 206.761 192.722 -2.673 -2.742 1.404 N1 C4J 3 C4J C2 C3 C 0 1 N N N 131.431 206.955 194.032 -3.305 -1.793 0.689 C2 C4J 4 C4J N3 N2 N 0 1 N N N 130.761 206.039 194.749 -2.630 -1.014 -0.176 N3 C4J 5 C4J C4 C4 C 0 1 N N N 130.313 204.948 194.186 -1.301 -1.174 -0.341 C4 C4J 6 C4J C1 C5 C 0 1 N N N 132.334 207.734 191.923 -3.434 -3.575 2.338 C1 C4J 7 C4J "C1'" C6 C 0 1 N N S 129.999 203.478 192.180 0.861 -2.368 0.239 "C1'" C4J 8 C4J "C2'" C7 C 0 1 N N R 128.532 203.116 192.344 1.167 -2.857 -1.193 "C2'" C4J 9 C4J C3 C8 C 0 1 N N N 130.544 206.237 196.159 -3.342 0.011 -0.943 C3 C4J 10 C4J "C3'" C9 C 0 1 N N S 127.891 203.765 191.113 2.471 -2.085 -1.533 "C3'" C4J 11 C4J C31 C10 C 0 1 N N N 131.747 205.737 196.930 -3.345 1.325 -0.158 C31 C4J 12 C4J C32 C11 C 0 1 N N S 131.678 206.257 198.347 -4.088 2.396 -0.958 C32 C4J 13 C4J C34 C12 C 0 1 N N N 131.962 207.754 198.311 -4.197 3.653 -0.135 C34 C4J 14 C4J "C4'" C13 C 0 1 N N S 129.058 204.083 190.171 2.228 -0.752 -0.780 "C4'" C4J 15 C4J "C5'" C14 C 0 1 N N N 128.963 203.573 188.766 3.561 -0.079 -0.449 "C5'" C4J 16 C4J N33 N3 N 0 1 N N N 130.349 206.020 198.866 -3.349 2.684 -2.195 N33 C4J 17 C4J O2 O1 O 0 1 N N N 131.827 207.936 194.545 -4.503 -1.638 0.827 O2 C4J 18 C4J "O2'" O2 O 0 1 N N N 128.423 201.709 192.270 1.388 -4.269 -1.211 "O2'" C4J 19 C4J "O3'" O3 O 0 1 N N N 126.885 202.974 190.514 3.620 -2.763 -1.022 "O3'" C4J 20 C4J O35 O4 O 0 1 N N N 131.058 208.491 198.785 -5.142 3.754 0.814 O35 C4J 21 C4J O36 O5 O 0 1 N N N 133.051 208.155 197.825 -3.435 4.570 -0.328 O36 C4J 22 C4J O4 O6 O 0 1 N N N 129.736 204.172 194.867 -0.690 -0.469 -1.123 O4 C4J 23 C4J "O4'" O7 O 0 1 N N N 130.227 203.542 190.812 1.542 -1.122 0.426 "O4'" C4J 24 C4J "O5'" O8 O 0 1 N N N 130.213 203.694 188.123 3.315 1.171 0.199 "O5'" C4J 25 C4J OP1 O9 O 0 1 N N N 132.110 205.210 188.122 5.412 1.409 1.584 OP1 C4J 26 C4J OP2 O10 O 0 1 N N N 129.797 206.221 187.849 5.310 2.693 -0.587 OP2 C4J 27 C4J P P1 P 0 1 N N N 130.733 205.080 187.550 4.494 2.151 0.691 P C4J 28 C4J H1 H1 H 0 1 N N N 131.356 205.509 191.107 -0.826 -3.704 1.839 H1 C4J 29 C4J H2 H2 H 0 1 N N N 132.636 208.580 192.558 -3.448 -3.101 3.319 H2 C4J 30 C4J H3 H3 H 0 1 N N N 133.228 207.266 191.486 -4.456 -3.688 1.975 H3 C4J 31 C4J H4 H4 H 0 1 N N N 131.679 208.096 191.117 -2.966 -4.556 2.415 H4 C4J 32 C4J H5 H5 H 0 1 N N N 130.584 202.644 192.595 1.219 -3.099 0.964 H5 C4J 33 C4J H6 H6 H 0 1 N N N 128.118 203.532 193.274 0.364 -2.583 -1.877 H6 C4J 34 C4J H7 H7 H 0 1 N N N 130.399 207.309 196.361 -2.843 0.161 -1.900 H7 C4J 35 C4J H8 H8 H 0 1 N N N 129.649 205.680 196.474 -4.369 -0.311 -1.115 H8 C4J 36 C4J H9 H9 H 0 1 N N N 127.453 204.722 191.433 2.561 -1.919 -2.606 H9 C4J 37 C4J H10 H10 H 0 1 N N N 131.746 204.637 196.941 -3.843 1.175 0.799 H10 C4J 38 C4J H11 H11 H 0 1 N N N 132.668 206.098 196.450 -2.318 1.647 0.014 H11 C4J 39 C4J H12 H12 H 0 1 N N N 132.434 205.752 198.967 -5.087 2.036 -1.207 H12 C4J 40 C4J H13 H13 H 0 1 N N N 129.157 205.178 190.127 1.606 -0.087 -1.380 H13 C4J 41 C4J H14 H14 H 0 1 N N N 128.212 204.159 188.216 4.139 -0.723 0.213 H14 C4J 42 C4J H15 H15 H 0 1 N N N 128.663 202.515 188.782 4.120 0.093 -1.368 H15 C4J 43 C4J H16 H16 H 0 1 N N N 130.292 206.361 199.804 -2.420 3.019 -1.992 H16 C4J 44 C4J H17 H17 H 0 1 N N N 129.679 206.497 198.297 -3.318 1.872 -2.795 H17 C4J 45 C4J H19 H19 H 0 1 N N N 128.824 201.319 193.038 1.585 -4.624 -2.089 H19 C4J 46 C4J H20 H20 H 0 1 N N N 126.193 202.811 191.144 3.749 -3.649 -1.388 H20 C4J 47 C4J H21 H21 H 0 1 N N N 131.324 209.401 198.720 -5.173 4.579 1.316 H21 C4J 48 C4J H23 H23 H 0 1 N N N 130.247 206.871 188.376 4.769 3.190 -1.216 H23 C4J 49 C4J OP3 OP3 O 0 1 N Y N 130.944 204.750 185.991 3.859 3.396 1.490 OP3 C4J 50 C4J H24 H24 H 0 1 N N N 131.873 204.715 185.797 4.513 4.029 1.816 H24 C4J 51 # 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 C4J P OP2 SING N N 1 C4J P OP1 DOUB N N 2 C4J P "O5'" SING N N 3 C4J "O5'" "C5'" SING N N 4 C4J "C5'" "C4'" SING N N 5 C4J "C4'" "O4'" SING N N 6 C4J "C4'" "C3'" SING N N 7 C4J "O3'" "C3'" SING N N 8 C4J "O4'" "C1'" SING N N 9 C4J "C3'" "C2'" SING N N 10 C4J C1 N1 SING N N 11 C4J C6 N1 SING N N 12 C4J C6 C5 DOUB N N 13 C4J "C1'" "C2'" SING N N 14 C4J "C1'" C5 SING N N 15 C4J "O2'" "C2'" SING N N 16 C4J N1 C2 SING N N 17 C4J C5 C4 SING N N 18 C4J C2 O2 DOUB N N 19 C4J C2 N3 SING N N 20 C4J C4 N3 SING N N 21 C4J C4 O4 DOUB N N 22 C4J N3 C3 SING N N 23 C4J C3 C31 SING N N 24 C4J C31 C32 SING N N 25 C4J O36 C34 DOUB N N 26 C4J C34 C32 SING N N 27 C4J C34 O35 SING N N 28 C4J C32 N33 SING N N 29 C4J C6 H1 SING N N 30 C4J C1 H2 SING N N 31 C4J C1 H3 SING N N 32 C4J C1 H4 SING N N 33 C4J "C1'" H5 SING N N 34 C4J "C2'" H6 SING N N 35 C4J C3 H7 SING N N 36 C4J C3 H8 SING N N 37 C4J "C3'" H9 SING N N 38 C4J C31 H10 SING N N 39 C4J C31 H11 SING N N 40 C4J C32 H12 SING N N 41 C4J "C4'" H13 SING N N 42 C4J "C5'" H14 SING N N 43 C4J "C5'" H15 SING N N 44 C4J N33 H16 SING N N 45 C4J N33 H17 SING N N 46 C4J "O2'" H19 SING N N 47 C4J "O3'" H20 SING N N 48 C4J O35 H21 SING N N 49 C4J OP2 H23 SING N N 50 C4J P OP3 SING N N 51 C4J OP3 H24 SING N N 52 # 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 C4J SMILES ACDLabs 12.01 "C=1N(C(=O)N(CCC(N)C(O)=O)C(C=1C2C(C(C(O2)COP(=O)(O)O)O)O)=O)C" C4J InChI InChI 1.03 "InChI=1S/C14H22N3O11P/c1-16-4-6(12(20)17(14(16)23)3-2-7(15)13(21)22)11-10(19)9(18)8(28-11)5-27-29(24,25)26/h4,7-11,18-19H,2-3,5,15H2,1H3,(H,21,22)(H2,24,25,26)/t7-,8-,9+,10+,11-/m0/s1" C4J InChIKey InChI 1.03 BVRIEBGMUPJSJF-DAWVFNFOSA-N C4J SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@@H]2O[C@@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N(CC[C@H](N)C(O)=O)C1=O" C4J SMILES CACTVS 3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N(CC[CH](N)C(O)=O)C1=O" C4J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)O)O)O" C4J SMILES "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)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 C4J "SYSTEMATIC NAME" ACDLabs 12.01 "(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol" C4J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{S})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic 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 C4J "Create component" 2017-09-13 RCSB C4J "Initial release" 2017-12-06 RCSB #