data_UBI # _chem_comp.id UBI _chem_comp.name ;2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-11-07 _chem_comp.pdbx_modified_date 2012-11-16 _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 407.313 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UBI _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 4HQX _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 UBI P P P 0 1 N N N 20.963 -2.702 6.980 5.662 1.677 0.204 P UBI 1 UBI N1 N1 N 0 1 N N N 18.925 -7.912 7.794 -0.504 -0.949 0.099 N1 UBI 2 UBI C2 C2 C 0 1 N N N 19.294 -9.254 8.004 -0.426 -0.652 -1.208 C2 UBI 3 UBI O2 O2 O 0 1 N N N 19.592 -9.939 7.007 0.643 -0.765 -1.774 O2 UBI 4 UBI N3 N3 N 0 1 N N N 19.322 -9.793 9.243 -1.493 -0.233 -1.910 N3 UBI 5 UBI C4 C4 C 0 1 N N N 18.994 -9.046 10.315 -2.695 -0.096 -1.312 C4 UBI 6 UBI O4 O4 O 0 1 N N N 19.017 -9.543 11.459 -3.664 0.282 -1.943 O4 UBI 7 UBI C5 C5 C 0 1 N N N 18.603 -7.623 10.106 -2.808 -0.415 0.120 C5 UBI 8 UBI C6 C6 C 0 1 N N N 18.599 -7.122 8.815 -1.673 -0.840 0.783 C6 UBI 9 UBI "C1'" "C1'" C 0 1 N N R 18.927 -7.391 6.429 0.697 -1.406 0.802 "C1'" UBI 10 UBI "C2'" "C2'" C 0 1 N N N 17.642 -6.660 6.032 1.156 -2.761 0.229 "C2'" UBI 11 UBI C21 C21 C 0 1 N N N 18.209 -6.690 11.211 -4.091 -0.285 0.826 C21 UBI 12 UBI O22 O22 O 0 1 N N N 17.784 -5.593 10.886 -4.190 -0.650 1.982 O22 UBI 13 UBI N23 N23 N 0 1 N N N 18.298 -7.048 12.491 -5.159 0.240 0.191 N23 UBI 14 UBI C24 C24 C 0 1 N N N 17.950 -6.227 13.647 -6.405 0.473 0.925 C24 UBI 15 UBI C25 C25 C 0 1 N N N 16.942 -6.949 14.544 -7.450 1.070 -0.021 C25 UBI 16 UBI C26 C26 C 0 1 N N N 16.634 -8.395 14.181 -8.787 1.198 0.711 C26 UBI 17 UBI C27 C27 C 0 1 N N N 15.650 -6.159 14.582 -6.987 2.453 -0.484 C27 UBI 18 UBI "C3'" "C3'" C 0 1 N N S 18.128 -5.674 4.990 2.599 -2.496 -0.262 "C3'" UBI 19 UBI "O3'" "O3'" O 0 1 N N N 17.817 -6.240 3.717 3.456 -3.595 0.056 "O3'" UBI 20 UBI "C4'" "C4'" C 0 1 N N R 19.644 -5.711 5.089 2.993 -1.235 0.549 "C4'" UBI 21 UBI "O4'" "O4'" O 0 1 N N N 19.960 -6.420 6.284 1.768 -0.469 0.600 "O4'" UBI 22 UBI "C5'" "C5'" C 0 1 N N N 20.304 -4.344 5.026 4.090 -0.451 -0.172 "C5'" UBI 23 UBI "O5'" "O5'" O 0 1 N N N 19.916 -3.612 6.163 4.515 0.639 0.649 "O5'" UBI 24 UBI OP1 OP1 O 0 1 N N N 22.351 -2.843 6.399 6.892 0.934 -0.146 OP1 UBI 25 UBI OP2 OP2 O 0 1 N N N 20.312 -1.349 7.148 5.159 2.516 -1.075 OP2 UBI 26 UBI OP3 OP3 O 0 1 N Y N 20.909 -3.481 8.382 5.972 2.687 1.419 OP3 UBI 27 UBI HN3 HN3 H 0 1 N N N 19.587 -10.750 9.364 -1.398 -0.028 -2.854 HN3 UBI 28 UBI H6 H6 H 0 1 N N N 18.332 -6.091 8.636 -1.714 -1.084 1.834 H6 UBI 29 UBI "H1'" "H1'" H 0 1 N N N 19.089 -8.219 5.723 0.488 -1.505 1.867 "H1'" UBI 30 UBI "H2'" "H2'" H 0 1 N N N 16.905 -7.357 5.606 1.151 -3.525 1.006 "H2'" UBI 31 UBI "H2'A" "H2'A" H 0 0 N N N 17.199 -6.140 6.894 0.516 -3.060 -0.602 "H2'A" UBI 32 UBI HN23 HN23 H 0 0 N N N 18.637 -7.970 12.679 -5.102 0.462 -0.751 HN23 UBI 33 UBI H24 H24 H 0 1 N N N 18.861 -6.015 14.226 -6.774 -0.472 1.324 H24 UBI 34 UBI H24A H24A H 0 0 N N N 17.509 -5.281 13.298 -6.220 1.167 1.745 H24A UBI 35 UBI H25 H25 H 0 1 N N N 17.356 -6.949 15.563 -7.570 0.418 -0.886 H25 UBI 36 UBI H26 H26 H 0 1 N N N 15.902 -8.804 14.893 -8.666 1.849 1.577 H26 UBI 37 UBI H26A H26A H 0 0 N N N 16.219 -8.437 13.163 -9.531 1.622 0.038 H26A UBI 38 UBI H26B H26B H 0 0 N N N 17.559 -8.989 14.225 -9.116 0.212 1.042 H26B UBI 39 UBI H27 H27 H 0 1 N N N 14.923 -6.675 15.226 -6.035 2.361 -1.006 H27 UBI 40 UBI H27A H27A H 0 0 N N N 15.847 -5.154 14.983 -7.732 2.878 -1.158 H27A UBI 41 UBI H27B H27B H 0 0 N N N 15.242 -6.074 13.564 -6.867 3.104 0.381 H27B UBI 42 UBI "H3'" "H3'" H 0 1 N N N 17.721 -4.664 5.143 2.615 -2.290 -1.333 "H3'" UBI 43 UBI "HO3'" "HO3'" H 0 0 N N N 18.106 -5.652 3.029 3.196 -4.429 -0.359 "HO3'" UBI 44 UBI "H4'" "H4'" H 0 1 N N N 20.013 -6.292 4.231 3.313 -1.510 1.554 "H4'" UBI 45 UBI "H5'" "H5'" H 0 1 N N N 21.398 -4.460 5.014 4.937 -1.109 -0.369 "H5'" UBI 46 UBI "H5'A" "H5'A" H 0 0 N N N 19.981 -3.817 4.116 3.702 -0.065 -1.115 "H5'A" UBI 47 UBI HOP2 HOP2 H 0 0 N N N 20.903 -0.672 6.841 4.355 3.029 -0.918 HOP2 UBI 48 UBI HOP3 HOP3 H 0 0 N Y N 21.757 -3.871 8.561 6.655 3.343 1.221 HOP3 UBI 49 # 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 UBI "O5'" P SING N N 1 UBI OP1 P DOUB N N 2 UBI P OP2 SING N N 3 UBI P OP3 SING N N 4 UBI "C1'" N1 SING N N 5 UBI N1 C2 SING N N 6 UBI N1 C6 SING N N 7 UBI O2 C2 DOUB N N 8 UBI C2 N3 SING N N 9 UBI N3 C4 SING N N 10 UBI N3 HN3 SING N N 11 UBI C5 C4 SING N N 12 UBI C4 O4 DOUB N N 13 UBI C6 C5 DOUB N N 14 UBI C5 C21 SING N N 15 UBI C6 H6 SING N N 16 UBI "C2'" "C1'" SING N N 17 UBI "O4'" "C1'" SING N N 18 UBI "C1'" "H1'" SING N N 19 UBI "C3'" "C2'" SING N N 20 UBI "C2'" "H2'" SING N N 21 UBI "C2'" "H2'A" SING N N 22 UBI O22 C21 DOUB N N 23 UBI C21 N23 SING N N 24 UBI N23 C24 SING N N 25 UBI N23 HN23 SING N N 26 UBI C24 C25 SING N N 27 UBI C24 H24 SING N N 28 UBI C24 H24A SING N N 29 UBI C26 C25 SING N N 30 UBI C25 C27 SING N N 31 UBI C25 H25 SING N N 32 UBI C26 H26 SING N N 33 UBI C26 H26A SING N N 34 UBI C26 H26B SING N N 35 UBI C27 H27 SING N N 36 UBI C27 H27A SING N N 37 UBI C27 H27B SING N N 38 UBI "O3'" "C3'" SING N N 39 UBI "C3'" "C4'" SING N N 40 UBI "C3'" "H3'" SING N N 41 UBI "O3'" "HO3'" SING N N 42 UBI "C5'" "C4'" SING N N 43 UBI "C4'" "O4'" SING N N 44 UBI "C4'" "H4'" SING N N 45 UBI "C5'" "O5'" SING N N 46 UBI "C5'" "H5'" SING N N 47 UBI "C5'" "H5'A" SING N N 48 UBI OP2 HOP2 SING N N 49 UBI OP3 HOP3 SING N N 50 # 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 UBI SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(C(=O)NCC(C)C)=C1)CC2O" UBI InChI InChI 1.03 "InChI=1S/C14H22N3O9P/c1-7(2)4-15-12(19)8-5-17(14(21)16-13(8)20)11-3-9(18)10(26-11)6-25-27(22,23)24/h5,7,9-11,18H,3-4,6H2,1-2H3,(H,15,19)(H,16,20,21)(H2,22,23,24)/t9-,10+,11+/m0/s1" UBI InChIKey InChI 1.03 MVIGTWKPLCSGIV-HBNTYKKESA-N UBI SMILES_CANONICAL CACTVS 3.370 "CC(C)CNC(=O)C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" UBI SMILES CACTVS 3.370 "CC(C)CNC(=O)C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" UBI SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)CNC(=O)C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" UBI SMILES "OpenEye OEToolkits" 1.7.6 "CC(C)CNC(=O)C1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=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 UBI "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; UBI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[5-(2-methylpropylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-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 UBI "Create component" 2012-11-07 RCSB UBI "Initial release" 2012-11-16 RCSB #