data_LTP # _chem_comp.id LTP _chem_comp.name "4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N3 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-12-14 _chem_comp.pdbx_modified_date 2014-08-22 _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 387.177 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LTP _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 4I8U _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 LTP OAE OAE O 0 1 N N N 0.935 -12.153 20.273 4.643 2.518 0.589 OAE LTP 1 LTP PAF PAF P 0 1 N N N -0.313 -12.845 20.785 4.969 1.264 -0.367 PAF LTP 2 LTP OAG OAG O 0 1 N N N -0.151 -13.578 22.091 5.434 1.799 -1.813 OAG LTP 3 LTP OBB OBB O 0 1 N N N -1.064 -13.609 19.725 6.054 0.455 0.232 OBB LTP 4 LTP OAH OAH O 0 1 N N N -1.290 -11.649 21.180 3.649 0.356 -0.530 OAH LTP 5 LTP PAI PAI P 0 1 N N N -1.758 -10.642 20.041 2.886 -0.689 0.428 PAI LTP 6 LTP OAJ OAJ O 0 1 N N N -0.639 -9.661 19.780 2.774 -0.119 1.790 OAJ LTP 7 LTP OAK OAK O 0 1 N N N -3.075 -10.102 20.507 3.717 -2.067 0.489 OAK LTP 8 LTP OAL OAL O 0 1 N N N -2.012 -11.585 18.730 1.413 -0.975 -0.156 OAL LTP 9 LTP CAM CAM C 0 1 N N N -1.708 -11.178 17.380 0.449 -1.781 0.524 CAM LTP 10 LTP CAN CAN C 0 1 N N S -2.957 -10.814 16.567 -0.836 -1.847 -0.303 CAN LTP 11 LTP OAO OAO O 0 1 N N N -4.151 -11.250 17.217 -1.460 -0.546 -0.366 OAO LTP 12 LTP CAP CAP C 0 1 N N R -2.988 -11.397 15.155 -1.878 -2.751 0.392 CAP LTP 13 LTP O12 O12 O 0 1 N N N -2.649 -10.404 14.194 -1.867 -4.060 -0.182 O12 LTP 14 LTP CAQ CAQ C 0 1 N N N -4.410 -11.835 14.924 -3.227 -2.049 0.120 CAQ LTP 15 LTP CAR CAR C 0 1 N N S -5.133 -11.612 16.248 -2.840 -0.802 -0.707 CAR LTP 16 LTP N1 N1 N 0 1 N N N -5.801 -12.871 16.562 -3.679 0.339 -0.332 N1 LTP 17 LTP C2 C2 C 0 1 N N N -6.957 -13.164 15.951 -5.015 0.263 -0.475 C2 LTP 18 LTP O2 O2 O 0 1 N N N -7.502 -12.373 15.143 -5.514 -0.758 -0.916 O2 LTP 19 LTP C6 C6 C 0 1 N N N -5.171 -13.788 17.524 -3.102 1.469 0.164 C6 LTP 20 LTP C5 C5 C 0 1 N N N -5.922 -15.028 17.703 -3.888 2.517 0.507 C5 LTP 21 LTP C4 C4 C 0 1 N N N -7.117 -15.239 17.026 -5.284 2.408 0.340 C4 LTP 22 LTP NAX NAX N 0 1 N N N -7.820 -16.389 17.211 -6.105 3.458 0.680 NAX LTP 23 LTP N3 N3 N 0 1 N N N -7.573 -14.313 16.187 -5.801 1.286 -0.142 N3 LTP 24 LTP H1 H1 H 0 1 N N N 1.034 -12.324 19.344 3.940 3.093 0.258 H1 LTP 25 LTP H2 H2 H 0 1 N N N -0.564 -14.431 22.029 6.225 2.354 -1.791 H2 LTP 26 LTP H3 H3 H 0 1 N N N -3.022 -9.156 20.579 3.829 -2.497 -0.369 H3 LTP 27 LTP H4 H4 H 0 1 N N N -1.189 -12.005 16.873 0.846 -2.787 0.659 H4 LTP 28 LTP H5 H5 H 0 1 N N N -1.047 -10.299 17.419 0.232 -1.343 1.499 H5 LTP 29 LTP H6 H6 H 0 1 N N N -2.983 -9.718 16.474 -0.622 -2.214 -1.307 H6 LTP 30 LTP H7 H7 H 0 1 N N N -2.311 -12.262 15.093 -1.684 -2.804 1.463 H7 LTP 31 LTP H8 H8 H 0 1 N N N -1.753 -10.122 14.332 -2.503 -4.670 0.217 H8 LTP 32 LTP H9 H9 H 0 1 N N N -4.872 -11.232 14.129 -3.887 -2.698 -0.454 H9 LTP 33 LTP H10 H10 H 0 1 N N N -4.443 -12.898 14.644 -3.699 -1.753 1.057 H10 LTP 34 LTP H11 H11 H 0 1 N N N -5.874 -10.808 16.127 -2.937 -1.010 -1.773 H11 LTP 35 LTP H12 H12 H 0 1 N N N -4.250 -13.568 18.043 -2.030 1.528 0.283 H12 LTP 36 LTP H13 H13 H 0 1 N N N -5.544 -15.790 18.369 -3.452 3.423 0.903 H13 LTP 37 LTP H14 H14 H 0 1 N N N -8.677 -16.536 16.717 -5.725 4.276 1.036 H14 LTP 38 LTP H15 H15 H 0 1 N N N -7.480 -17.087 17.841 -7.065 3.380 0.564 H15 LTP 39 # 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 LTP O12 CAP SING N N 1 LTP CAQ CAP SING N N 2 LTP CAQ CAR SING N N 3 LTP O2 C2 DOUB N N 4 LTP CAP CAN SING N N 5 LTP C2 N3 SING N N 6 LTP C2 N1 SING N N 7 LTP N3 C4 DOUB N N 8 LTP CAR N1 SING N N 9 LTP CAR OAO SING N N 10 LTP N1 C6 SING N N 11 LTP CAN OAO SING N N 12 LTP CAN CAM SING N N 13 LTP C4 NAX SING N N 14 LTP C4 C5 SING N N 15 LTP CAM OAL SING N N 16 LTP C6 C5 DOUB N N 17 LTP OAL PAI SING N N 18 LTP OBB PAF DOUB N N 19 LTP OAJ PAI DOUB N N 20 LTP PAI OAK SING N N 21 LTP PAI OAH SING N N 22 LTP OAE PAF SING N N 23 LTP PAF OAH SING N N 24 LTP PAF OAG SING N N 25 LTP OAE H1 SING N N 26 LTP OAG H2 SING N N 27 LTP OAK H3 SING N N 28 LTP CAM H4 SING N N 29 LTP CAM H5 SING N N 30 LTP CAN H6 SING N N 31 LTP CAP H7 SING N N 32 LTP O12 H8 SING N N 33 LTP CAQ H9 SING N N 34 LTP CAQ H10 SING N N 35 LTP CAR H11 SING N N 36 LTP C6 H12 SING N N 37 LTP C5 H13 SING N N 38 LTP NAX H14 SING N N 39 LTP NAX H15 SING N N 40 # 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 LTP SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O" LTP InChI InChI 1.03 "InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m1/s1" LTP InChIKey InChI 1.03 FTDHDKPUHBLBTL-CHKWXVPMSA-N LTP SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(O)=O)O2" LTP SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2" LTP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O" LTP SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=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 LTP "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one" LTP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-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 LTP "Create component" 2012-12-14 RCSB LTP "Initial release" 2014-08-27 RCSB #