data_C31 # _chem_comp.id C31 _chem_comp.name ;2'-O-3-AMINOPROPYL CYTIDINE-5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H21 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id C _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 380.291 _chem_comp.one_letter_code C _chem_comp.three_letter_code C31 _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 C31 P P P 0 1 N N N 71.172 62.767 -7.895 -0.345 0.414 -4.757 P C31 1 C31 O1P O1P O 0 1 N N N 70.918 61.550 -6.873 0.565 -0.080 -5.989 O1P C31 2 C31 O2P O2P O 0 1 N N N 70.766 62.500 -9.257 0.073 1.774 -4.350 O2P C31 3 C31 O3P O3P O 0 1 N Y N 72.771 62.671 -7.865 -1.890 0.442 -5.210 O3P C31 4 C31 "O5'" O5* O 0 1 N N N 70.244 63.946 -7.322 -0.167 -0.596 -3.517 "O5'" C31 5 C31 "C5'" C5* C 0 1 N N N 70.238 64.428 -5.876 -0.996 -0.105 -2.462 "C5'" C31 6 C31 "C4'" C4* C 0 1 N N R 69.638 63.475 -4.893 -0.873 -1.025 -1.246 "C4'" C31 7 C31 "O4'" O4* O 0 1 N N N 70.492 63.359 -3.738 0.482 -1.027 -0.766 "O4'" C31 8 C31 "C3'" C3* C 0 1 N N R 68.241 63.885 -4.446 -1.763 -0.504 -0.101 "C3'" C31 9 C31 "O3'" O3* O 0 1 N N N 67.277 62.874 -4.713 -2.743 -1.481 0.257 "O3'" C31 10 C31 "C2'" C2* C 0 1 N N R 68.334 64.013 -2.925 -0.778 -0.270 1.069 "C2'" C31 11 C31 "O2'" O2* O 0 1 N N N 67.604 63.007 -2.251 -1.346 -0.700 2.307 "O2'" C31 12 C31 "C1'" C1* C 0 1 N N R 69.831 63.886 -2.621 0.421 -1.166 0.669 "C1'" C31 13 C31 N1 N1 N 0 1 N N N 70.501 65.128 -2.183 1.659 -0.685 1.287 N1 C31 14 C31 C2 C2 C 0 1 N N N 71.412 65.736 -3.035 2.057 0.584 1.086 C2 C31 15 C31 O2 O2 O 0 1 N N N 71.711 65.293 -4.117 1.378 1.323 0.394 O2 C31 16 C31 N3 N3 N 0 1 N N N 71.974 66.897 -2.561 3.175 1.049 1.641 N3 C31 17 C31 C4 C4 C 0 1 N N N 71.749 67.502 -1.345 3.933 0.266 2.398 C4 C31 18 C31 N4 N4 N 0 1 N N N 72.342 68.551 -1.069 5.088 0.757 2.961 N4 C31 19 C31 C5 C5 C 0 1 N N N 70.815 66.816 -0.507 3.546 -1.070 2.623 C5 C31 20 C31 C6 C6 C 0 1 N N N 70.233 65.679 -0.944 2.404 -1.527 2.058 C6 C31 21 C31 "CA'" CA* C 0 1 N N N 67.560 63.223 -0.844 -1.948 0.448 2.906 "CA'" C31 22 C31 "CB'" CB* C 0 1 N N N 66.678 64.263 -0.460 -2.579 0.055 4.244 "CB'" C31 23 C31 CC CC C 0 1 N N N 66.755 64.279 0.947 -3.224 1.285 4.885 CC C31 24 C31 "ND'" ND* N 0 1 N N N 66.097 65.372 1.483 -3.829 0.907 6.169 "ND'" C31 25 C31 H1P H1P H 0 1 N N N 71.184 61.725 -5.978 0.429 0.550 -6.709 H1P C31 26 C31 H3P H3P H 0 1 N N N 72.920 63.389 -8.468 -2.122 -0.460 -5.467 H3P C31 27 C31 "H5'1" 1H5* H 0 0 N N N 69.736 65.421 -5.804 -2.033 -0.081 -2.795 "H5'1" C31 28 C31 "H5'2" 2H5* H 0 0 N N N 71.270 64.707 -5.560 -0.679 0.901 -2.189 "H5'2" C31 29 C31 "H4'" H4* H 0 1 N N N 69.569 62.473 -5.377 -1.171 -2.038 -1.516 "H4'" C31 30 C31 "H3'" H3* H 0 1 N N N 67.942 64.854 -4.910 -2.245 0.430 -0.388 "H3'" C31 31 C31 HA HA H 0 1 N N N 66.406 63.130 -4.434 -3.326 -1.585 -0.506 HA C31 32 C31 "H2'" H2* H 0 1 N N N 67.970 65.018 -2.609 -0.480 0.777 1.122 "H2'" C31 33 C31 "H1'" H1* H 0 1 N N N 69.938 63.145 -1.795 0.233 -2.204 0.947 "H1'" C31 34 C31 H4N1 1H4N H 0 0 N N N 72.175 68.999 -0.168 5.351 1.677 2.804 H4N1 C31 35 C31 H4N2 2H4N H 0 0 N N N 73.008 69.040 -1.667 5.639 0.182 3.515 H4N2 C31 36 C31 H5 H5 H 0 1 N N N 70.571 67.214 0.492 4.151 -1.720 3.238 H5 C31 37 C31 H6 H6 H 0 1 N N N 69.512 65.168 -0.284 2.086 -2.547 2.216 H6 C31 38 C31 "HA'1" 1HA* H 0 0 N N N 68.583 63.404 -0.440 -2.719 0.842 2.243 "HA'1" C31 39 C31 "HA'2" 2HA* H 0 0 N N N 67.313 62.278 -0.307 -1.188 1.212 3.074 "HA'2" C31 40 C31 "HB'1" 1HB* H 0 0 N N N 65.643 64.156 -0.860 -1.809 -0.338 4.907 "HB'1" C31 41 C31 "HB'2" 2HB* H 0 0 N N N 66.893 65.246 -0.941 -3.339 -0.707 4.076 "HB'2" C31 42 C31 HCC1 1HCC H 0 0 N N N 67.813 64.229 1.297 -3.994 1.679 4.222 HCC1 C31 43 C31 HCC2 2HCC H 0 0 N N N 66.382 63.324 1.385 -2.464 2.048 5.052 HCC2 C31 44 C31 "HD'1" 1HD* H 0 0 N N N 66.033 66.298 1.061 -4.240 1.745 6.554 "HD'1" C31 45 C31 "HD'2" 2HD* H 0 0 N N N 66.392 65.907 2.300 -4.592 0.281 5.957 "HD'2" C31 46 # 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 C31 P O1P SING N N 1 C31 P O2P DOUB N N 2 C31 P O3P SING N N 3 C31 P "O5'" SING N N 4 C31 O1P H1P SING N N 5 C31 O3P H3P SING N N 6 C31 "O5'" "C5'" SING N N 7 C31 "C5'" "C4'" SING N N 8 C31 "C5'" "H5'1" SING N N 9 C31 "C5'" "H5'2" SING N N 10 C31 "C4'" "O4'" SING N N 11 C31 "C4'" "C3'" SING N N 12 C31 "C4'" "H4'" SING N N 13 C31 "O4'" "C1'" SING N N 14 C31 "C3'" "O3'" SING N N 15 C31 "C3'" "C2'" SING N N 16 C31 "C3'" "H3'" SING N N 17 C31 "O3'" HA SING N N 18 C31 "C2'" "O2'" SING N N 19 C31 "C2'" "C1'" SING N N 20 C31 "C2'" "H2'" SING N N 21 C31 "O2'" "CA'" SING N N 22 C31 "C1'" N1 SING N N 23 C31 "C1'" "H1'" SING N N 24 C31 N1 C2 SING N N 25 C31 N1 C6 SING N N 26 C31 C2 O2 DOUB N N 27 C31 C2 N3 SING N N 28 C31 N3 C4 DOUB N N 29 C31 C4 N4 SING N N 30 C31 C4 C5 SING N N 31 C31 N4 H4N1 SING N N 32 C31 N4 H4N2 SING N N 33 C31 C5 C6 DOUB N N 34 C31 C5 H5 SING N N 35 C31 C6 H6 SING N N 36 C31 "CA'" "CB'" SING N N 37 C31 "CA'" "HA'1" SING N N 38 C31 "CA'" "HA'2" SING N N 39 C31 "CB'" CC SING N N 40 C31 "CB'" "HB'1" SING N N 41 C31 "CB'" "HB'2" SING N N 42 C31 CC "ND'" SING N N 43 C31 CC HCC1 SING N N 44 C31 CC HCC2 SING N N 45 C31 "ND'" "HD'1" SING N N 46 C31 "ND'" "HD'2" SING N N 47 # 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 C31 SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2OCCCN)COP(=O)(O)O" C31 SMILES_CANONICAL CACTVS 3.341 "NCCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N" C31 SMILES CACTVS 3.341 "NCCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" C31 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCCN" C31 SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)OCCCN" C31 InChI InChI 1.03 "InChI=1S/C12H21N4O8P/c13-3-1-5-22-10-9(17)7(6-23-25(19,20)21)24-11(10)16-4-2-8(14)15-12(16)18/h2,4,7,9-11,17H,1,3,5-6,13H2,(H2,14,15,18)(H2,19,20,21)/t7-,9-,10-,11-/m1/s1" C31 InChIKey InChI 1.03 XUVXRCKZTRKVOD-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 C31 "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-(3-aminopropyl)cytidine 5'-(dihydrogen phosphate) ; C31 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-(3-aminopropoxy)-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 C31 "Create component" 1999-12-02 RCSB C31 "Modify descriptor" 2011-06-04 RCSB #