data_2BD # _chem_comp.id 2BD _chem_comp.name ;N1-(1-HYDROXY-3-BUTEN-2(S)-YL)-2'-DEOXYINOSINE MONO PHOSPHORIC ACID ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H19 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id DI _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-08-02 _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 402.296 _chem_comp.one_letter_code I _chem_comp.three_letter_code 2BD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1U6N _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 2BD P P P 0 1 N N N -1.600 9.651 14.492 -0.770 0.094 4.765 P 2BD 1 2BD OP1 O1P O 0 1 N N N -3.044 9.508 14.202 -2.269 0.097 4.837 OP1 2BD 2 2BD OP2 O2P O 0 1 N N N -0.889 10.949 14.508 -0.066 1.535 4.976 OP2 2BD 3 2BD OP3 O3P O 0 1 N Y N ? ? ? -0.035 -0.843 5.859 OP3 2BD 4 2BD "O5'" O5* O 0 1 N N N -0.606 8.405 14.623 -0.153 -0.433 3.364 "O5'" 2BD 5 2BD "C5'" C5* C 0 1 N N N -1.271 7.152 14.346 1.256 -0.466 3.216 "C5'" 2BD 6 2BD "C4'" C4* C 0 1 N N R -1.854 6.964 15.695 1.587 -0.994 1.827 "C4'" 2BD 7 2BD "O4'" O4* O 0 1 N N N -1.385 5.845 16.513 1.032 -0.080 0.857 "O4'" 2BD 8 2BD "C1'" C1* C 0 1 N N R -0.899 6.360 17.861 2.110 0.511 0.111 "C1'" 2BD 9 2BD O6 O6 O 0 1 N N N 4.675 4.396 18.058 1.437 6.069 -1.874 O6 2BD 10 2BD C6 C6 C 0 1 N N N 3.958 5.373 17.922 1.866 4.930 -2.017 C6 2BD 11 2BD C5 C5 C 0 1 Y N N 2.591 5.136 18.063 1.671 3.896 -1.032 C5 2BD 12 2BD N7 N7 N 0 1 Y N N 1.895 4.014 18.203 1.022 3.980 0.166 N7 2BD 13 2BD C8 C8 C 0 1 Y N N 0.610 4.349 18.249 1.129 2.767 0.672 C8 2BD 14 2BD N9 N9 N 0 1 Y N N 0.445 5.629 18.143 1.820 1.916 -0.155 N9 2BD 15 2BD C4 C4 C 0 1 Y N N 1.686 6.177 18.045 2.173 2.637 -1.257 C4 2BD 16 2BD N3 N3 N 0 1 N N N 2.129 7.434 17.939 2.864 2.179 -2.322 N3 2BD 17 2BD C2 C2 C 0 1 N N N 3.405 7.751 17.798 3.045 3.112 -3.213 C2 2BD 18 2BD N1 N1 N 0 1 N N N 4.448 6.757 17.695 2.599 4.447 -3.126 N1 2BD 19 2BD CAN CAN C 0 1 N N S 6.039 7.323 17.511 2.903 5.359 -4.215 CAN 2BD 20 2BD CAL CAL C 0 1 N N N 7.038 6.309 17.117 4.397 5.454 -4.329 CAL 2BD 21 2BD CAM CAM C 0 1 N N N 8.089 6.507 17.755 5.091 6.577 -4.108 CAM 2BD 22 2BD CAO CAO C 0 1 N N N 5.661 8.217 16.221 2.277 4.878 -5.523 CAO 2BD 23 2BD OAP OAP O 0 1 N N N 5.622 9.592 15.805 0.864 4.804 -5.367 OAP 2BD 24 2BD "C2'" C2* C 0 1 N N N -0.495 7.746 17.557 3.381 0.276 0.915 "C2'" 2BD 25 2BD "C3'" C3* C 0 1 N N S -1.384 8.112 16.505 3.088 -1.057 1.564 "C3'" 2BD 26 2BD "O3'" O3* O 0 1 N N N -2.015 9.349 16.220 3.364 -2.089 0.619 "O3'" 2BD 27 2BD HOP2 2HOP H 0 0 N N N 0.038 11.040 14.694 -0.337 2.088 5.739 HOP2 2BD 28 2BD HOP3 3HOP H 0 0 N N N 0.927 0.091 0.186 -0.311 -0.781 6.799 HOP3 2BD 29 2BD "H5'" 1H5* H 0 1 N N N -0.602 6.318 14.165 1.653 0.542 3.338 "H5'" 2BD 30 2BD "H5''" 2H5* H 0 0 N N N -2.048 7.299 13.537 1.681 -1.122 3.977 "H5''" 2BD 31 2BD "H4'" H4* H 0 1 N N N -2.953 6.981 15.620 1.104 -1.966 1.683 "H4'" 2BD 32 2BD "H1'" H1* H 0 1 N N N -1.706 6.218 18.391 2.154 0.023 -0.868 "H1'" 2BD 33 2BD H8 H8 H 0 1 N N N -0.150 3.680 18.269 0.732 2.447 1.626 H8 2BD 34 2BD H2 H2 H 0 1 N N N 3.653 8.783 17.669 3.596 2.888 -4.140 H2 2BD 35 2BD HAN HAN H 0 1 N N N 6.482 8.029 17.995 2.463 6.322 -3.930 HAN 2BD 36 2BD HAL2 2HAL H 0 0 N N N 6.646 5.318 17.345 4.942 4.557 -4.613 HAL2 2BD 37 2BD HAM1 1HAM H 0 0 N N N 8.276 5.543 18.196 6.171 6.604 -4.200 HAM1 2BD 38 2BD HAM2 2HAM H 0 0 N N N 8.978 6.813 17.307 4.580 7.492 -3.828 HAM2 2BD 39 2BD HAO1 1HAO H 0 0 N N N 4.783 8.582 16.336 2.646 3.887 -5.811 HAO1 2BD 40 2BD HAO2 2HAO H 0 0 N N N 6.627 8.856 16.170 2.485 5.581 -6.337 HAO2 2BD 41 2BD HAP HAP H 0 1 N N N 4.694 9.834 15.496 0.701 4.393 -4.503 HAP 2BD 42 2BD "H2'" 1H2* H 0 1 N N N 0.518 7.791 17.219 3.498 1.050 1.683 "H2'" 2BD 43 2BD "H2''" 2H2* H 0 0 N N N -0.633 8.363 18.429 4.270 0.278 0.277 "H2''" 2BD 44 2BD "H3'" H3* H 0 1 N N N -0.489 8.307 15.867 3.687 -1.252 2.457 "H3'" 2BD 45 2BD "HO3'" H3T H 0 0 N Y N -1.713 10.085 16.739 2.519 -2.525 0.432 "HO3'" 2BD 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 2BD P OP1 DOUB N N 1 2BD P OP2 SING N N 2 2BD P OP3 SING N N 3 2BD P "O5'" SING N N 4 2BD OP2 HOP2 SING N N 5 2BD OP3 HOP3 SING N N 6 2BD "O5'" "C5'" SING N N 7 2BD "C5'" "C4'" SING N N 8 2BD "C5'" "H5'" SING N N 9 2BD "C5'" "H5''" SING N N 10 2BD "C4'" "O4'" SING N N 11 2BD "C4'" "C3'" SING N N 12 2BD "C4'" "H4'" SING N N 13 2BD "O4'" "C1'" SING N N 14 2BD "C1'" N9 SING N N 15 2BD "C1'" "C2'" SING N N 16 2BD "C1'" "H1'" SING N N 17 2BD O6 C6 DOUB N N 18 2BD C6 C5 SING N N 19 2BD C6 N1 SING N N 20 2BD C5 N7 SING Y N 21 2BD C5 C4 DOUB Y N 22 2BD N7 C8 DOUB Y N 23 2BD C8 N9 SING Y N 24 2BD C8 H8 SING N N 25 2BD N9 C4 SING Y N 26 2BD C4 N3 SING N N 27 2BD N3 C2 DOUB N N 28 2BD C2 N1 SING N N 29 2BD C2 H2 SING N N 30 2BD N1 CAN SING N N 31 2BD CAN CAL SING N N 32 2BD CAN CAO SING N N 33 2BD CAN HAN SING N N 34 2BD CAL CAM DOUB N N 35 2BD CAL HAL2 SING N N 36 2BD CAM HAM1 SING N N 37 2BD CAM HAM2 SING N N 38 2BD CAO OAP SING N N 39 2BD CAO HAO1 SING N N 40 2BD CAO HAO2 SING N N 41 2BD OAP HAP SING N N 42 2BD "C2'" "C3'" SING N N 43 2BD "C2'" "H2'" SING N N 44 2BD "C2'" "H2''" SING N N 45 2BD "C3'" "O3'" SING N N 46 2BD "C3'" "H3'" SING N N 47 2BD "O3'" "HO3'" SING N N 48 # 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 2BD SMILES ACDLabs 10.04 "O=C1c2ncn(c2N=CN1C(\C=C)CO)C3OC(C(O)C3)COP(=O)(O)O" 2BD SMILES_CANONICAL CACTVS 3.341 "OC[C@H](C=C)N1C=Nc2n(cnc2C1=O)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3" 2BD SMILES CACTVS 3.341 "OC[CH](C=C)N1C=Nc2n(cnc2C1=O)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3" 2BD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C=C[C@@H](CO)N1C=Nc2c(ncn2[C@H]3CC([C@H](O3)COP(=O)(O)O)O)C1=O" 2BD SMILES "OpenEye OEToolkits" 1.5.0 "C=CC(CO)N1C=Nc2c(ncn2C3CC(C(O3)COP(=O)(O)O)O)C1=O" 2BD InChI InChI 1.03 "InChI=1S/C14H19N4O8P/c1-2-8(4-19)17-7-16-13-12(14(17)21)15-6-18(13)11-3-9(20)10(26-11)5-25-27(22,23)24/h2,6-11,19-20H,1,3-5H2,(H2,22,23,24)/t8-,9-,10+,11+/m0/s1" 2BD InChIKey InChI 1.03 LXPLTWVTQXOUTK-UKKRHICBSA-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 2BD "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-1-[(1S)-1-(hydroxymethyl)prop-2-en-1-yl]inosine 5'-(dihydrogen phosphate) ; 2BD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,5R)-3-hydroxy-5-[1-[(2S)-1-hydroxybut-3-en-2-yl]-6-oxo-purin-9-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 2BD "Create component" 2004-08-02 RCSB 2BD "Modify descriptor" 2011-06-04 RCSB #