data_CDF # _chem_comp.id CDF _chem_comp.name "4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-ALPHA-D-ARABINOFURANOSYL}PYRIMIDIN-2(1H)-ONE" _chem_comp.type non-polymer _chem_comp.pdbx_type ? _chem_comp.formula "C9 H15 N3 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-04-23 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 403.176 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CDF _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 2VSI _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 CDF O3B O3B O 0 1 N N N -15.604 -14.502 4.270 5.970 -0.906 1.158 O3B CDF 1 CDF PB PB P 0 1 N N N -15.355 -14.868 2.822 5.375 -1.126 -0.179 PB CDF 2 CDF O1B O1B O 0 1 N N N -16.590 -15.353 2.089 6.151 -0.228 -1.266 O1B CDF 3 CDF O2B O2B O 0 1 N N N -14.146 -15.758 2.614 5.506 -2.681 -0.575 O2B CDF 4 CDF O3A O3A O 0 1 N N N -15.026 -13.452 2.094 3.820 -0.710 -0.149 O3A CDF 5 CDF PA PA P 0 1 N N R -13.668 -12.593 2.311 3.010 0.548 0.446 PA CDF 6 CDF O1A O1A O 0 1 N N N -13.701 -11.391 1.391 2.911 0.414 2.047 O1A CDF 7 CDF O2A O2A O 0 1 N N N -13.507 -12.355 3.793 3.719 1.800 0.099 O2A CDF 8 CDF "O5'" "O5'" O 0 1 N N N -12.536 -13.623 1.782 1.528 0.579 -0.183 "O5'" CDF 9 CDF "C5'" "C5'" C 0 1 N N N -11.166 -13.252 1.625 0.598 1.634 0.068 "C5'" CDF 10 CDF "C4'" "C4'" C 0 1 N N R -10.565 -13.740 0.310 -0.707 1.352 -0.679 "C4'" CDF 11 CDF "O4'" "O4'" O 0 1 N N N -11.566 -13.944 -0.696 -1.342 0.193 -0.125 "O4'" CDF 12 CDF "C3'" "C3'" C 0 1 N N S -9.640 -12.646 -0.203 -1.676 2.541 -0.508 "C3'" CDF 13 CDF "O3'" "O3'" O 0 1 N N N -8.295 -13.119 -0.308 -1.672 3.371 -1.671 "O3'" CDF 14 CDF "C2'" "C2'" C 0 1 N N S -10.222 -12.216 -1.536 -3.046 1.829 -0.342 "C2'" CDF 15 CDF "O2'" "O2'" O 0 1 N N N -10.134 -10.794 -1.635 -3.946 2.619 0.438 "O2'" CDF 16 CDF "C1'" "C1'" C 0 1 N N S -11.662 -12.719 -1.419 -2.622 0.549 0.422 "C1'" CDF 17 CDF N1 N1 N 0 1 N N N -12.513 -12.729 -2.633 -3.590 -0.525 0.191 N1 CDF 18 CDF C2 C2 C 0 1 N N N -12.106 -13.097 -3.946 -4.863 -0.379 0.602 C2 CDF 19 CDF O2 O2 O 0 1 N N N -10.955 -13.488 -4.209 -5.197 0.651 1.165 O2 CDF 20 CDF N3 N3 N 0 1 N N N -12.989 -13.031 -4.968 -5.765 -1.339 0.405 N3 CDF 21 CDF C4 C4 C 0 1 N N N -14.259 -12.613 -4.767 -5.428 -2.469 -0.204 C4 CDF 22 CDF N4 N4 N 0 1 N N N -15.117 -12.558 -5.805 -6.368 -3.454 -0.403 N4 CDF 23 CDF C6 C6 C 0 1 N N N -13.778 -12.314 -2.446 -3.199 -1.666 -0.443 C6 CDF 24 CDF C5 C5 C 0 1 N N N -14.684 -12.242 -3.499 -4.102 -2.654 -0.646 C5 CDF 25 CDF H1B H1B H 0 1 N N N -17.305 -15.454 2.706 5.813 -0.322 -2.168 H1B CDF 26 CDF H2B H2B H 0 1 N N N -14.045 -15.944 1.688 6.418 -3.002 -0.612 H2B CDF 27 CDF H1A H1A H 0 1 N N N -13.708 -10.595 1.909 2.457 -0.386 2.348 H1A CDF 28 CDF "H5'1" "H5'1" H 0 0 N N N -11.100 -12.154 1.649 0.399 1.697 1.138 "H5'1" CDF 29 CDF "H5'2" "H5'2" H 0 0 N N N -10.599 -13.721 2.443 1.018 2.579 -0.279 "H5'2" CDF 30 CDF "H4'" "H4'" H 0 1 N N N -10.050 -14.694 0.498 -0.500 1.190 -1.737 "H4'" CDF 31 CDF "H3'" "H3'" H 0 1 N N N -9.583 -11.789 0.485 -1.426 3.121 0.381 "H3'" CDF 32 CDF "H1'" "H1'" H 0 1 N N N -12.265 -11.973 -0.880 -2.532 0.757 1.488 "H1'" CDF 33 CDF HA HA H 0 1 N N N -8.066 -13.224 -1.224 -2.266 4.133 -1.613 HA CDF 34 CDF "H2'" "H2'" H 0 1 N N N -9.719 -12.605 -2.434 -3.481 1.583 -1.310 "H2'" CDF 35 CDF HB HB H 0 1 N N N -10.114 -10.416 -0.764 -4.155 3.479 0.047 HB CDF 36 CDF H41N H41N H 0 0 N N N -16.010 -12.231 -5.495 -7.279 -3.323 -0.098 H41N CDF 37 CDF H42N H42N H 0 0 N N N -14.894 -12.807 -6.747 -6.119 -4.279 -0.848 H42N CDF 38 CDF H6 H6 H 0 1 N N N -14.098 -12.030 -1.455 -2.178 -1.782 -0.777 H6 CDF 39 CDF H5 H5 H 0 1 N N N -15.696 -11.905 -3.333 -3.813 -3.568 -1.143 H5 CDF 40 # 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 CDF O3B PB DOUB N N 1 CDF PB O1B SING N N 2 CDF PB O2B SING N N 3 CDF PB O3A SING N N 4 CDF O3A PA SING N N 5 CDF PA O1A SING N N 6 CDF PA O2A DOUB N N 7 CDF PA "O5'" SING N N 8 CDF "O5'" "C5'" SING N N 9 CDF "C5'" "C4'" SING N N 10 CDF "C4'" "O4'" SING N N 11 CDF "C4'" "C3'" SING N N 12 CDF "O4'" "C1'" SING N N 13 CDF "C3'" "O3'" SING N N 14 CDF "C3'" "C2'" SING N N 15 CDF "C2'" "O2'" SING N N 16 CDF "C2'" "C1'" SING N N 17 CDF "C1'" N1 SING N N 18 CDF N1 C2 SING N N 19 CDF N1 C6 SING N N 20 CDF C2 O2 DOUB N N 21 CDF C2 N3 SING N N 22 CDF N3 C4 DOUB N N 23 CDF C4 N4 SING N N 24 CDF C4 C5 SING N N 25 CDF O1B H1B SING N N 26 CDF O2B H2B SING N N 27 CDF O1A H1A SING N N 28 CDF "C5'" "H5'1" SING N N 29 CDF "C5'" "H5'2" SING N N 30 CDF "C4'" "H4'" SING N N 31 CDF "C3'" "H3'" SING N N 32 CDF "C1'" "H1'" SING N N 33 CDF "O3'" HA SING N N 34 CDF "C2'" "H2'" SING N N 35 CDF "O2'" HB SING N N 36 CDF N4 H41N SING N N 37 CDF N4 H42N SING N N 38 CDF C6 C5 DOUB N N 39 CDF C5 H5 SING N N 40 CDF C6 H6 SING N N 41 # 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 CDF SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O" CDF SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2O" CDF SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O" CDF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@@H]2[C@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O" CDF SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O" CDF InChI InChI 1.03 "InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7+,8+/m1/s1" CDF InChIKey InChI 1.03 ZWIADYZPOWUWEW-GVYWOMJSSA-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 CDF "SYSTEMATIC NAME" ACDLabs 10.04 "4-amino-1-{5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-alpha-D-arabinofuranosyl}pyrimidin-2(1H)-one" CDF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4S,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen 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 CDF "Create component" 2008-04-23 EBI CDF "Modify descriptor" 2011-06-04 RCSB #