data_D4D # _chem_comp.id D4D _chem_comp.name ;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N2 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-08-23 _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 384.173 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D4D _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 1F3F _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 D4D PA PA P 0 1 N N S -13.113 45.306 33.353 -2.869 0.575 0.008 PA D4D 1 D4D O1A O1A O 0 1 N N N -14.247 46.212 33.053 -2.505 -0.335 -1.101 O1A D4D 2 D4D O2A O2A O 0 1 N N N -12.504 44.504 32.260 -3.697 1.827 -0.574 O2A D4D 3 D4D O3A O3A O 0 1 N N N -11.972 46.148 34.084 -3.775 -0.218 1.077 O3A D4D 4 D4D PB PB P 0 1 N N N -11.430 47.635 33.877 -4.781 -1.150 0.234 PB D4D 5 D4D O1B O1B O 0 1 N N N -12.592 48.400 33.354 -4.009 -2.479 -0.243 O1B D4D 6 D4D O2B O2B O 0 1 N N N -10.236 47.492 33.002 -5.264 -0.408 -0.952 O2B D4D 7 D4D O3B O3B O 0 1 N N N -11.229 48.128 35.267 -6.035 -1.560 1.157 O3B D4D 8 D4D "O5'" "O5'" O 0 1 N N N -13.582 44.314 34.510 -1.530 1.105 0.728 "O5'" D4D 9 D4D "C5'" "C5'" C 0 1 N N N -14.433 44.768 35.562 -0.718 1.692 -0.291 "C5'" D4D 10 D4D "C4'" "C4'" C 0 1 N N S -13.936 44.255 36.894 0.578 2.218 0.330 "C4'" D4D 11 D4D "O4'" "O4'" O 0 1 N N N -14.012 42.807 36.902 1.377 1.123 0.818 "O4'" D4D 12 D4D "C3'" "C3'" C 0 1 N N N -12.493 44.568 37.217 1.421 2.904 -0.720 "C3'" D4D 13 D4D "C2'" "C2'" C 0 1 N N N -11.875 43.435 37.592 2.669 2.528 -0.561 "C2'" D4D 14 D4D "C1'" "C1'" C 0 1 N N R -12.863 42.290 37.537 2.730 1.566 0.603 "C1'" D4D 15 D4D N1 N1 N 0 1 Y N N -12.361 41.166 36.726 3.589 0.426 0.274 N1 D4D 16 D4D C2 C2 C 0 1 Y N N -12.011 39.993 37.363 3.238 -0.406 -0.723 C2 D4D 17 D4D O2 O2 O 0 1 N N N -12.112 39.829 38.570 2.211 -0.203 -1.340 O2 D4D 18 D4D N3 N3 N 0 1 Y N N -11.535 39.011 36.527 4.009 -1.461 -1.047 N3 D4D 19 D4D C4 C4 C 0 1 Y N N -11.377 39.086 35.155 5.154 -1.698 -0.376 C4 D4D 20 D4D O4 O4 O 0 1 N N N -10.923 38.125 34.539 5.852 -2.652 -0.669 O4 D4D 21 D4D C5 C5 C 0 1 Y N N -11.774 40.341 34.555 5.533 -0.833 0.679 C5 D4D 22 D4D C5M C5M C 0 1 N N N -11.648 40.513 33.073 6.805 -1.078 1.448 C5M D4D 23 D4D C6 C6 C 0 1 Y N N -12.239 41.303 35.360 4.741 0.218 0.983 C6 D4D 24 D4D H2AO OH2A H 0 0 N N N -11.777 43.923 32.452 -3.913 2.393 0.179 H2AO D4D 25 D4D H1BO OH1B H 0 0 N N N -12.269 49.285 33.230 -3.711 -2.932 0.558 H1BO D4D 26 D4D H3BO OH3B H 0 0 N N N -10.906 49.013 35.143 -6.611 -2.116 0.615 H3BO D4D 27 D4D "H5'1" "1H5'" H 0 0 N N N -14.544 45.877 35.558 -1.258 2.515 -0.757 "H5'1" D4D 28 D4D "H5'2" "2H5'" H 0 0 N N N -15.499 44.495 35.382 -0.480 0.941 -1.044 "H5'2" D4D 29 D4D "H4'C" "CH4'" H 0 0 N N N -14.584 44.766 37.642 0.352 2.910 1.142 "H4'C" D4D 30 D4D "H3'C" "CH3'" H 0 0 N N N -11.946 45.525 37.182 1.059 3.589 -1.473 "H3'C" D4D 31 D4D "H2'C" "CH2'" H 0 0 N N N -10.809 43.443 37.877 3.508 2.849 -1.162 "H2'C" D4D 32 D4D "H1'C" "CH1'" H 0 0 N N N -13.054 41.905 38.565 3.105 2.074 1.492 "H1'C" D4D 33 D4D HN3 HN3 H 0 1 N N N -11.270 38.132 36.972 3.741 -2.051 -1.769 HN3 D4D 34 D4D H5M1 1H5M H 0 0 N N N -11.954 41.480 32.610 6.595 -1.720 2.303 H5M1 D4D 35 D4D H5M2 2H5M H 0 0 N N N -10.597 40.290 32.774 7.534 -1.563 0.799 H5M2 D4D 36 D4D H5M3 3H5M H 0 0 N N N -12.198 39.685 32.568 7.207 -0.127 1.798 H5M3 D4D 37 D4D H66 6H6 H 0 1 N N N -12.534 42.250 34.877 5.016 0.891 1.782 H66 D4D 38 # 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 D4D PA O1A DOUB N N 1 D4D PA O2A SING N N 2 D4D PA O3A SING N N 3 D4D PA "O5'" SING N N 4 D4D O2A H2AO SING N N 5 D4D O3A PB SING N N 6 D4D PB O1B SING N N 7 D4D PB O2B DOUB N N 8 D4D PB O3B SING N N 9 D4D O1B H1BO SING N N 10 D4D O3B H3BO SING N N 11 D4D "O5'" "C5'" SING N N 12 D4D "C5'" "C4'" SING N N 13 D4D "C5'" "H5'1" SING N N 14 D4D "C5'" "H5'2" SING N N 15 D4D "C4'" "O4'" SING N N 16 D4D "C4'" "C3'" SING N N 17 D4D "C4'" "H4'C" SING N N 18 D4D "O4'" "C1'" SING N N 19 D4D "C3'" "C2'" DOUB N N 20 D4D "C3'" "H3'C" SING N N 21 D4D "C2'" "C1'" SING N N 22 D4D "C2'" "H2'C" SING N N 23 D4D "C1'" N1 SING N N 24 D4D "C1'" "H1'C" SING N N 25 D4D N1 C2 SING Y N 26 D4D N1 C6 SING Y N 27 D4D C2 O2 DOUB N N 28 D4D C2 N3 SING Y N 29 D4D N3 C4 SING Y N 30 D4D N3 HN3 SING N N 31 D4D C4 O4 DOUB N N 32 D4D C4 C5 SING Y N 33 D4D C5 C5M SING N N 34 D4D C5 C6 DOUB Y N 35 D4D C5M H5M1 SING N N 36 D4D C5M H5M2 SING N N 37 D4D C5M H5M3 SING N N 38 D4D C6 H66 SING N N 39 # 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 D4D SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)C=C2" D4D SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O" D4D SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)C=C2)C(=O)NC1=O" D4D SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)CO[P@](=O)(O)OP(=O)(O)O" D4D SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)OP(=O)(O)O" D4D InChI InChI 1.03 "InChI=1S/C10H14N2O10P2/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(21-8)5-20-24(18,19)22-23(15,16)17/h2-4,7-8H,5H2,1H3,(H,18,19)(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1" D4D InChIKey InChI 1.03 LXCAIISEDMYORY-JGVFFNPUSA-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 D4D "SYSTEMATIC NAME" ACDLabs 10.04 "[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl trihydrogen diphosphate" D4D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-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 D4D "Create component" 2000-08-23 RCSB D4D "Modify descriptor" 2011-06-04 RCSB #