data_U31 # _chem_comp.id U31 _chem_comp.name ;2'-O-3-AMINOPROPYL 2'-DEOXYURIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H20 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-12-02 _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 381.276 _chem_comp.one_letter_code U _chem_comp.three_letter_code U31 _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 1D9D _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 U31 P P P 0 1 N N N 78.402 64.461 -7.570 -0.364 0.409 -4.758 P U31 1 U31 O1P O1P O 0 1 N N N 78.558 64.343 -9.021 0.544 -0.084 -5.992 O1P U31 2 U31 O2P O2P O 0 1 N N N 78.178 65.782 -6.991 0.051 1.771 -4.353 O2P U31 3 U31 O3P O3P O 0 1 N Y N 79.792 63.774 -6.963 -1.911 0.431 -5.206 O3P U31 4 U31 "O5'" O5* O 0 1 N N N 77.048 63.680 -7.374 -0.179 -0.599 -3.517 "O5'" U31 5 U31 "C5'" C5* C 0 1 N N N 76.037 64.180 -8.282 -1.006 -0.110 -2.460 "C5'" U31 6 U31 "C4'" C4* C 0 1 N N R 74.667 64.040 -7.819 -0.876 -1.029 -1.244 "C4'" U31 7 U31 "O4'" O4* O 0 1 N N N 73.973 65.225 -8.236 0.480 -1.026 -0.768 "O4'" U31 8 U31 "C3'" C3* C 0 1 N N R 73.998 62.921 -8.631 -1.764 -0.509 -0.097 "C3'" U31 9 U31 "O3'" O3* O 0 1 N N N 72.771 62.671 -7.865 -2.740 -1.488 0.265 "O3'" U31 10 U31 "C2'" C2* C 0 1 N N R 73.686 63.690 -9.947 -0.776 -0.271 1.070 "C2'" U31 11 U31 "O2'" O2* O 0 1 N N N 72.945 62.837 -10.824 -1.339 -0.701 2.311 "O2'" U31 12 U31 "C1'" C1* C 0 1 N N R 73.077 64.975 -9.289 0.424 -1.164 0.668 "C1'" U31 13 U31 N1 N1 N 0 1 N N N 72.832 66.313 -9.861 1.662 -0.678 1.281 N1 U31 14 U31 C2 C2 C 0 1 N N N 72.445 67.406 -9.128 2.054 0.592 1.076 C2 U31 15 U31 O2 O2 O 0 1 N N N 72.261 67.371 -7.986 1.371 1.325 0.387 O2 U31 16 U31 N3 N3 N 0 1 N N N 72.178 68.568 -9.840 3.184 1.066 1.631 N3 U31 17 U31 C4 C4 C 0 1 N N N 72.297 68.753 -11.149 3.952 0.266 2.398 C4 U31 18 U31 O4 O4 O 0 1 N N N 71.987 69.831 -11.667 4.978 0.692 2.897 O4 U31 19 U31 C5 C5 C 0 1 N N N 72.770 67.649 -11.795 3.555 -1.074 2.618 C5 U31 20 U31 C6 C6 C 0 1 N N N 73.061 66.507 -11.147 2.413 -1.522 2.053 C6 U31 21 U31 "CA'" CA* C 0 1 N N N 72.979 61.327 -10.725 -1.943 0.446 2.911 "CA'" U31 22 U31 "CB'" CB* C 0 1 N N N 73.674 60.562 -9.707 -2.568 0.051 4.250 "CB'" U31 23 U31 CC CC C 0 1 N N N 73.038 59.348 -9.386 -3.215 1.280 4.893 CC U31 24 U31 "ND'" ND* N 0 1 N N N 73.098 58.999 -8.017 -3.815 0.901 6.179 "ND'" U31 25 U31 H1P H1P H 0 1 N N N 78.703 63.483 -9.397 0.404 0.546 -6.712 H1P U31 26 U31 H3P H3P H 0 1 N N N 79.690 63.850 -6.021 -2.141 -0.472 -5.461 H3P U31 27 U31 "H5'1" 1H5* H 0 0 N N N 76.154 63.706 -9.285 -2.044 -0.090 -2.790 "H5'1" U31 28 U31 "H5'2" 2H5* H 0 0 N N N 76.247 65.243 -8.542 -0.691 0.897 -2.189 "H5'2" U31 29 U31 "H4'" H4* H 0 1 N N N 74.602 63.869 -6.719 -1.172 -2.043 -1.512 "H4'" U31 30 U31 "H3'" H3* H 0 1 N N N 74.637 62.018 -8.773 -2.250 0.423 -0.383 "H3'" U31 31 U31 HA HA H 0 1 N N N 72.357 61.979 -8.367 -3.326 -1.595 -0.496 HA U31 32 U31 "H2'" H2* H 0 1 N N N 74.648 63.962 -10.440 -0.481 0.777 1.121 "H2'" U31 33 U31 "H1'" H1* H 0 1 N N N 72.119 64.658 -8.815 0.240 -2.201 0.947 "H1'" U31 34 U31 H3 H3 H 0 1 N N N 71.854 69.368 -9.297 3.450 1.986 1.476 H3 U31 35 U31 H5 H5 H 0 1 N N N 72.919 67.694 -12.887 4.157 -1.730 3.229 H5 U31 36 U31 H6 H6 H 0 1 N N N 73.518 65.685 -11.723 2.094 -2.542 2.209 H6 U31 37 U31 "HA'1" 1HA* H 0 0 N N N 73.347 60.953 -11.709 -2.717 0.836 2.250 "HA'1" U31 38 U31 "HA'2" 2HA* H 0 0 N N N 71.917 60.987 -10.708 -1.185 1.211 3.075 "HA'2" U31 39 U31 "HB'1" 1HB* H 0 0 N N N 73.835 61.178 -8.791 -1.794 -0.339 4.911 "HB'1" U31 40 U31 "HB'2" 2HB* H 0 0 N N N 74.735 60.386 -10.001 -3.326 -0.714 4.086 "HB'2" U31 41 U31 HCC1 1HCC H 0 0 N N N 73.440 58.521 -10.016 -3.989 1.671 4.232 HCC1 U31 42 U31 HCC2 2HCC H 0 0 N N N 71.980 59.359 -9.738 -2.457 2.046 5.057 HCC2 U31 43 U31 "HD'1" 1HD* H 0 0 N N N 73.093 59.786 -7.368 -4.227 1.738 6.564 "HD'1" U31 44 U31 "HD'2" 2HD* H 0 0 N N N 73.994 58.625 -7.704 -4.576 0.273 5.970 "HD'2" U31 45 # 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 U31 P O1P SING N N 1 U31 P O2P DOUB N N 2 U31 P O3P SING N N 3 U31 P "O5'" SING N N 4 U31 O1P H1P SING N N 5 U31 O3P H3P SING N N 6 U31 "O5'" "C5'" SING N N 7 U31 "C5'" "C4'" SING N N 8 U31 "C5'" "H5'1" SING N N 9 U31 "C5'" "H5'2" SING N N 10 U31 "C4'" "O4'" SING N N 11 U31 "C4'" "C3'" SING N N 12 U31 "C4'" "H4'" SING N N 13 U31 "O4'" "C1'" SING N N 14 U31 "C3'" "O3'" SING N N 15 U31 "C3'" "C2'" SING N N 16 U31 "C3'" "H3'" SING N N 17 U31 "O3'" HA SING N N 18 U31 "C2'" "O2'" SING N N 19 U31 "C2'" "C1'" SING N N 20 U31 "C2'" "H2'" SING N N 21 U31 "O2'" "CA'" SING N N 22 U31 "C1'" N1 SING N N 23 U31 "C1'" "H1'" SING N N 24 U31 N1 C2 SING N N 25 U31 N1 C6 SING N N 26 U31 C2 O2 DOUB N N 27 U31 C2 N3 SING N N 28 U31 N3 C4 SING N N 29 U31 N3 H3 SING N N 30 U31 C4 O4 DOUB N N 31 U31 C4 C5 SING N N 32 U31 C5 C6 DOUB N N 33 U31 C5 H5 SING N N 34 U31 C6 H6 SING N N 35 U31 "CA'" "CB'" SING N N 36 U31 "CA'" "HA'1" SING N N 37 U31 "CA'" "HA'2" SING N N 38 U31 "CB'" CC SING N N 39 U31 "CB'" "HB'1" SING N N 40 U31 "CB'" "HB'2" SING N N 41 U31 CC "ND'" SING N N 42 U31 CC HCC1 SING N N 43 U31 CC HCC2 SING N N 44 U31 "ND'" "HD'1" SING N N 45 U31 "ND'" "HD'2" SING N N 46 # 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 U31 SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2OCCCN)COP(=O)(O)O" U31 SMILES_CANONICAL CACTVS 3.341 "NCCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" U31 SMILES CACTVS 3.341 "NCCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" U31 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCCN" U31 SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCCN" U31 InChI InChI 1.03 "InChI=1S/C12H20N3O9P/c13-3-1-5-22-10-9(17)7(6-23-25(19,20)21)24-11(10)15-4-2-8(16)14-12(15)18/h2,4,7,9-11,17H,1,3,5-6,13H2,(H,14,16,18)(H2,19,20,21)/t7-,9-,10-,11-/m1/s1" U31 InChIKey InChI 1.03 BYBLQLKEQYUZOM-QCNRFFRDSA-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 U31 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-(3-aminopropyl)uridine 5'-(dihydrogen phosphate) ; U31 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-(3-aminopropoxy)-5-(2,4-dioxopyrimidin-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 U31 "Create component" 1999-12-02 RCSB U31 "Modify descriptor" 2011-06-04 RCSB #