data_0R8 # _chem_comp.id 0R8 _chem_comp.name "[(2S,5R)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2H)-yl}tetrahydrofuran-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H18 N3 O6 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-04-27 _chem_comp.pdbx_modified_date 2013-04-19 _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 415.336 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 0R8 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4ELV _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 0R8 "O5'" "O5'" O 0 1 N N N 24.677 -15.915 -9.693 -2.987 2.624 -0.190 "O5'" 0R8 1 0R8 P P P 0 1 N N N 25.337 -14.474 -9.407 -2.186 4.000 -0.430 P 0R8 2 0R8 OP1 OP1 O 0 1 N N N 24.403 -13.639 -8.421 -2.251 4.830 0.793 OP1 0R8 3 0R8 OP2 OP2 O 0 1 N N N 25.651 -13.742 -10.778 -0.647 3.671 -0.774 OP2 0R8 4 0R8 "C1'" "C1'" C 0 1 N N R 23.788 -19.679 -8.754 -3.497 -1.672 0.034 "C1'" 0R8 5 0R8 N1 N1 N 0 1 N N N 23.425 -19.305 -7.398 -2.235 -2.393 -0.144 N1 0R8 6 0R8 C6 C6 C 0 1 N N N 23.623 -18.056 -6.908 -1.059 -1.717 -0.047 C6 0R8 7 0R8 C5 C5 C 0 1 N N N 23.327 -17.805 -5.626 0.125 -2.409 -0.217 C5 0R8 8 0R8 C1 C1 C 0 1 N N N 23.509 -16.499 -5.058 1.388 -1.742 -0.124 C1 0R8 9 0R8 C3 C3 C 0 1 N N N 23.564 -15.430 -4.516 2.424 -1.195 -0.049 C3 0R8 10 0R8 N3 N3 N 0 1 N N N 22.638 -20.009 -5.235 -1.145 -4.421 -0.569 N3 0R8 11 0R8 C4 C4 C 0 1 N N N 22.807 -18.854 -4.735 0.048 -3.848 -0.493 C4 0R8 12 0R8 C2 C2 C 0 1 N N N 22.950 -20.280 -6.608 -2.258 -3.712 -0.394 C2 0R8 13 0R8 O2 O2 O 0 1 N N N 22.718 -21.401 -7.016 -3.335 -4.279 -0.467 O2 0R8 14 0R8 N4 N4 N 0 1 N N N 22.581 -18.607 -3.428 1.192 -4.588 -0.671 N4 0R8 15 0R8 "O4'" "O4'" O 0 1 N N N 24.824 -18.828 -9.233 -3.319 -0.291 -0.301 "O4'" 0R8 16 0R8 "C4'" "C4'" C 0 1 N N S 24.477 -18.238 -10.500 -3.646 0.534 0.829 "C4'" 0R8 17 0R8 "C3'" "C3'" C 0 1 N N N 22.940 -18.187 -10.417 -3.444 -0.376 2.066 "C3'" 0R8 18 0R8 "C2'" "C2'" C 0 1 N N N 22.646 -19.571 -9.793 -3.938 -1.743 1.512 "C2'" 0R8 19 0R8 "C5'" "C5'" C 0 1 N N N 25.133 -16.846 -10.670 -2.706 1.739 0.896 "C5'" 0R8 20 0R8 C01 C01 C 0 1 Y N N 23.469 -14.197 -3.784 3.688 -0.528 0.043 C01 0R8 21 0R8 C02 C02 C 0 1 Y N N 24.478 -13.231 -3.822 3.738 0.844 0.314 C02 0R8 22 0R8 C03 C03 C 0 1 Y N N 24.333 -12.044 -3.097 4.944 1.479 0.402 C03 0R8 23 0R8 C04 C04 C 0 1 Y N N 23.177 -11.837 -2.331 6.128 0.759 0.221 C04 0R8 24 0R8 C05 C05 C 0 1 Y N N 22.164 -12.803 -2.293 6.080 -0.611 -0.050 C05 0R8 25 0R8 C C C 0 1 Y N N 22.312 -13.985 -3.023 4.875 -1.249 -0.131 C 0R8 26 0R8 C7 C7 C 0 1 N N N 23.016 -10.622 -1.573 7.392 1.426 0.313 C7 0R8 27 0R8 C8 C8 C 0 1 N N N 22.860 -9.615 -0.932 8.428 1.973 0.388 C8 0R8 28 0R8 HOP2 HOP2 H 0 0 N N N 25.218 -12.896 -10.792 -0.528 3.129 -1.566 HOP2 0R8 29 0R8 "H1'" "H1'" H 0 1 N N N 24.143 -20.720 -8.754 -4.266 -2.110 -0.602 "H1'" 0R8 30 0R8 H6 H6 H 0 1 N N N 24.014 -17.275 -7.543 -1.051 -0.656 0.157 H6 0R8 31 0R8 H41 H41 H 0 1 N N N 22.272 -19.343 -2.826 2.060 -4.159 -0.614 H41 0R8 32 0R8 H42 H42 H 0 1 N N N 22.722 -17.688 -3.061 1.131 -5.538 -0.854 H42 0R8 33 0R8 H7 H7 H 0 1 N N N 24.779 -18.889 -11.333 -4.683 0.865 0.769 H7 0R8 34 0R8 "H3'" "H3'" H 0 1 N N N 22.595 -17.368 -9.769 -2.392 -0.424 2.351 "H3'" 0R8 35 0R8 "H3''" "H3''" H 0 0 N N N 22.483 -18.085 -11.412 -4.060 -0.046 2.902 "H3''" 0R8 36 0R8 "H2'" "H2'" H 0 1 N N N 21.658 -19.594 -9.310 -5.022 -1.825 1.592 "H2'" 0R8 37 0R8 "H2''" "H2''" H 0 0 N N N 22.706 -20.373 -10.544 -3.446 -2.570 2.025 "H2''" 0R8 38 0R8 "H5'" "H5'" H 0 1 N N N 26.224 -16.954 -10.575 -1.673 1.398 0.828 "H5'" 0R8 39 0R8 "H5''" "H5''" H 0 0 N N N 24.889 -16.459 -11.670 -2.854 2.263 1.840 "H5''" 0R8 40 0R8 H14 H14 H 0 1 N N N 25.368 -13.401 -4.410 2.823 1.400 0.454 H14 0R8 41 0R8 H15 H15 H 0 1 N N N 25.107 -11.291 -3.127 4.982 2.538 0.611 H15 0R8 42 0R8 H16 H16 H 0 1 N N N 21.275 -12.636 -1.704 6.995 -1.166 -0.190 H16 0R8 43 0R8 H17 H17 H 0 1 N N N 21.535 -14.735 -3.001 4.838 -2.309 -0.336 H17 0R8 44 0R8 H18 H18 H 0 1 N N N 22.723 -8.728 -0.368 9.355 2.462 0.455 H18 0R8 45 0R8 OP3 OP3 O 0 1 N Y N ? ? ? -2.851 4.800 -1.658 OP3 0R8 46 0R8 HOP3 H1 H 0 0 N Y N ? ? ? -2.417 5.641 -1.860 H1 0R8 47 # 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 0R8 OP2 P SING N N 1 0R8 "C5'" "C4'" SING N N 2 0R8 "C5'" "O5'" SING N N 3 0R8 "C4'" "C3'" SING N N 4 0R8 "C4'" "O4'" SING N N 5 0R8 "C3'" "C2'" SING N N 6 0R8 "C2'" "C1'" SING N N 7 0R8 "O5'" P SING N N 8 0R8 P OP1 DOUB N N 9 0R8 "O4'" "C1'" SING N N 10 0R8 "C1'" N1 SING N N 11 0R8 N1 C6 SING N N 12 0R8 N1 C2 SING N N 13 0R8 O2 C2 DOUB N N 14 0R8 C6 C5 DOUB N N 15 0R8 C2 N3 SING N N 16 0R8 C5 C1 SING N N 17 0R8 C5 C4 SING N N 18 0R8 N3 C4 DOUB N N 19 0R8 C1 C3 TRIP N N 20 0R8 C4 N4 SING N N 21 0R8 C3 C01 SING N N 22 0R8 C02 C01 DOUB Y N 23 0R8 C02 C03 SING Y N 24 0R8 C01 C SING Y N 25 0R8 C03 C04 DOUB Y N 26 0R8 C C05 DOUB Y N 27 0R8 C04 C05 SING Y N 28 0R8 C04 C7 SING N N 29 0R8 C7 C8 TRIP N N 30 0R8 OP2 HOP2 SING N N 31 0R8 "C1'" "H1'" SING N N 32 0R8 C6 H6 SING N N 33 0R8 N4 H41 SING N N 34 0R8 N4 H42 SING N N 35 0R8 "C4'" H7 SING N N 36 0R8 "C3'" "H3'" SING N N 37 0R8 "C3'" "H3''" SING N N 38 0R8 "C2'" "H2'" SING N N 39 0R8 "C2'" "H2''" SING N N 40 0R8 "C5'" "H5'" SING N N 41 0R8 "C5'" "H5''" SING N N 42 0R8 C02 H14 SING N N 43 0R8 C03 H15 SING N N 44 0R8 C05 H16 SING N N 45 0R8 C H17 SING N N 46 0R8 C8 H18 SING N N 47 0R8 P OP3 SING N N 48 0R8 OP3 HOP3 SING N N 49 # 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 0R8 SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(N2C(=O)N=C(N)C(C#Cc1ccc(C#C)cc1)=C2)CC3" 0R8 InChI InChI 1.03 "InChI=1S/C19H18N3O6P/c1-2-13-3-5-14(6-4-13)7-8-15-11-22(19(23)21-18(15)20)17-10-9-16(28-17)12-27-29(24,25)26/h1,3-6,11,16-17H,9-10,12H2,(H2,20,21,23)(H2,24,25,26)/t16-,17+/m0/s1" 0R8 InChIKey InChI 1.03 IXTAGUCYLSQFGM-DLBZAZTESA-N 0R8 SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3CC[C@@H](CO[P](O)(O)=O)O3" 0R8 SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[CH]3CC[CH](CO[P](O)(O)=O)O3" 0R8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)[C@H]3CC[C@H](O3)COP(=O)(O)O" 0R8 SMILES "OpenEye OEToolkits" 1.7.6 "C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)C3CCC(O3)COP(=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 0R8 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,5R)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2H)-yl}tetrahydrofuran-2-yl]methyl dihydrogen phosphate" 0R8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]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 0R8 "Create component" 2012-04-27 RCSB 0R8 "Initial release" 2013-04-24 RCSB #