data_8PI # _chem_comp.id 8PI _chem_comp.name "1-{[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]amino}-1,2-dideoxy-5-O-phosphono-D-erythro-pentitol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H18 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-09-23 _chem_comp.pdbx_modified_date 2022-07-29 _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 367.252 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8PI _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 7S9L _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 8PI "C1'" C1 C 0 1 N N N 19.546 27.959 22.007 -0.983 -0.425 -0.055 "C1'" 8PI 1 8PI C2 C2 C 0 1 N N N 17.786 29.488 18.948 -4.707 -2.139 -0.092 C2 8PI 2 8PI "C2'" C3 C 0 1 N N N 20.688 27.338 22.770 0.241 0.494 -0.064 "C2'" 8PI 3 8PI "C3'" C4 C 0 1 N N S 20.879 27.976 24.103 1.513 -0.350 0.034 "C3'" 8PI 4 8PI C4 C5 C 0 1 N N N 17.638 28.726 21.354 -3.410 -0.218 -0.157 C4 8PI 5 8PI "C4'" C6 C 0 1 N N R 20.298 27.010 25.125 2.738 0.557 -0.101 "C4'" 8PI 6 8PI C5 C7 C 0 1 N N S 16.208 29.078 21.435 -4.691 0.591 -0.253 C5 8PI 7 8PI "C5'" C8 C 0 1 N N N 18.783 27.145 25.240 4.011 -0.287 -0.004 "C5'" 8PI 8 8PI C6 C9 C 0 1 N N N 15.587 29.658 20.217 -5.982 -0.207 -0.254 C6 8PI 9 8PI C8 C10 C 0 1 N N N 15.122 29.981 23.486 -5.444 2.661 0.789 C8 8PI 10 8PI N1 N1 N 0 1 N N N 16.353 29.856 19.004 -5.878 -1.533 -0.171 N1 8PI 11 8PI N2 N2 N 0 1 N N N 18.602 29.678 17.770 -4.708 -3.505 -0.017 N2 8PI 12 8PI N3 N3 N 0 1 N N N 18.392 28.932 20.150 -3.524 -1.525 -0.084 N3 8PI 13 8PI N7 N4 N 0 1 N N N 15.461 28.856 22.651 -4.729 1.521 0.878 N7 8PI 14 8PI N9 N5 N 0 1 N N N 18.395 28.146 22.428 -2.201 0.383 -0.148 N9 8PI 15 8PI "O3'" O1 O 0 1 N N N 22.264 28.133 24.250 1.549 -1.014 1.298 "O3'" 8PI 16 8PI "O4'" O2 O 0 1 N N N 20.562 25.731 24.608 2.703 1.221 -1.366 "O4'" 8PI 17 8PI "O5'" O3 O 0 1 N N N 18.300 26.669 26.444 5.153 0.571 -0.012 "O5'" 8PI 18 8PI O6 O4 O 0 1 N N N 14.452 29.968 20.222 -7.065 0.340 -0.326 O6 8PI 19 8PI O8 O5 O 0 1 N N N 15.462 31.063 23.142 -6.054 2.916 -0.228 O8 8PI 20 8PI OP1 O6 O 0 1 N N N 19.494 24.376 26.785 6.809 -0.831 1.278 OP1 8PI 21 8PI OP2 O7 O 0 1 N N N 17.341 24.816 27.869 6.997 -0.846 -1.239 OP2 8PI 22 8PI P P1 P 0 1 N N N 18.152 25.054 26.628 6.664 0.021 0.076 P 8PI 23 8PI H1 H1 H 0 1 N N N 19.425 27.331 21.112 -0.932 -1.106 -0.904 H1 8PI 24 8PI H2 H2 H 0 1 N N N 19.908 28.955 21.711 -0.998 -1.000 0.871 H2 8PI 25 8PI H3 H3 H 0 1 N N N 20.478 26.268 22.915 0.256 1.069 -0.990 H3 8PI 26 8PI H4 H4 H 0 1 N N N 21.612 27.455 22.184 0.190 1.174 0.786 H4 8PI 27 8PI H5 H5 H 0 1 N N N 20.350 28.939 24.149 1.520 -1.091 -0.766 H5 8PI 28 8PI H6 H6 H 0 1 N N N 20.769 27.164 26.107 2.731 1.297 0.698 H6 8PI 29 8PI H7 H7 H 0 1 N N N 16.475 30.087 21.781 -4.656 1.176 -1.171 H7 8PI 30 8PI H8 H8 H 0 1 N N N 18.515 28.208 25.148 3.995 -0.862 0.922 H8 8PI 31 8PI H9 H9 H 0 1 N N N 18.315 26.577 24.423 4.061 -0.968 -0.853 H9 8PI 32 8PI H10 H10 H 0 1 N N N 14.571 29.841 24.404 -5.472 3.347 1.622 H10 8PI 33 8PI H11 H11 H 0 1 N N N 18.202 30.074 16.943 -5.548 -3.990 -0.024 H11 8PI 34 8PI H12 H12 H 0 1 N N N 19.566 29.413 17.782 -3.869 -3.988 0.043 H12 8PI 35 8PI H13 H13 H 0 1 N N N 15.182 27.932 22.911 -4.241 1.317 1.691 H13 8PI 36 8PI H14 H14 H 0 1 N N N 18.057 27.933 23.345 -2.139 1.349 -0.203 H14 8PI 37 8PI H15 H15 H 0 1 N Y N 22.450 28.539 25.089 1.545 -0.415 2.057 H15 8PI 38 8PI H16 H16 H 0 1 N N N 20.262 25.072 25.223 2.707 0.621 -2.125 H16 8PI 39 8PI H18 H18 H 0 1 N N N 17.845 24.293 28.482 6.922 -0.350 -2.066 H18 8PI 40 8PI OP3 O8 O 0 1 N Y N 17.493 24.381 25.391 7.683 1.264 0.173 O1 8PI 41 8PI H17 H17 H 0 1 N N N 18.079 23.721 25.040 8.613 1.006 0.229 H17 8PI 42 # 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 8PI N2 C2 SING N N 1 8PI C2 N1 DOUB N N 2 8PI C2 N3 SING N N 3 8PI N1 C6 SING N N 4 8PI N3 C4 DOUB N N 5 8PI C6 O6 DOUB N N 6 8PI C6 C5 SING N N 7 8PI C4 C5 SING N N 8 8PI C4 N9 SING N N 9 8PI C5 N7 SING N N 10 8PI "C1'" N9 SING N N 11 8PI "C1'" "C2'" SING N N 12 8PI N7 C8 SING N N 13 8PI "C2'" "C3'" SING N N 14 8PI O8 C8 DOUB N N 15 8PI "C3'" "O3'" SING N N 16 8PI "C3'" "C4'" SING N N 17 8PI "O4'" "C4'" SING N N 18 8PI "C4'" "C5'" SING N N 19 8PI "C5'" "O5'" SING N N 20 8PI "O5'" P SING N N 21 8PI P OP1 DOUB N N 22 8PI P OP2 SING N N 23 8PI "C1'" H1 SING N N 24 8PI "C1'" H2 SING N N 25 8PI "C2'" H3 SING N N 26 8PI "C2'" H4 SING N N 27 8PI "C3'" H5 SING N N 28 8PI "C4'" H6 SING N N 29 8PI C5 H7 SING N N 30 8PI "C5'" H8 SING N N 31 8PI "C5'" H9 SING N N 32 8PI C8 H10 SING N N 33 8PI N2 H11 SING N N 34 8PI N2 H12 SING N N 35 8PI N7 H13 SING N N 36 8PI N9 H14 SING N N 37 8PI "O3'" H15 SING N N 38 8PI "O4'" H16 SING N N 39 8PI OP2 H18 SING N N 40 8PI P OP3 SING N N 41 8PI OP3 H17 SING N N 42 # 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 8PI SMILES ACDLabs 12.01 "O=C1N=C(N)N=C(NCCC(O)C(O)COP(=O)(O)O)C1NC=O" 8PI InChI InChI 1.03 "InChI=1S/C10H18N5O8P/c11-10-14-8(7(13-4-16)9(19)15-10)12-2-1-5(17)6(18)3-23-24(20,21)22/h4-7,17-18H,1-3H2,(H,13,16)(H2,20,21,22)(H3,11,12,14,15,19)/t5-,6+,7-/m0/s1" 8PI InChIKey InChI 1.03 UQQLUYQUTNSKKT-XVMARJQXSA-N 8PI SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)[C@@H](NC=O)C(=N1)NCC[C@H](O)[C@H](O)CO[P](O)(O)=O" 8PI SMILES CACTVS 3.385 "NC1=NC(=O)[CH](NC=O)C(=N1)NCC[CH](O)[CH](O)CO[P](O)(O)=O" 8PI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CNC1=NC(=NC(=O)C1NC=O)N)[C@@H]([C@@H](COP(=O)(O)O)O)O" 8PI SMILES "OpenEye OEToolkits" 2.0.7 "C(CNC1=NC(=NC(=O)C1NC=O)N)C(C(COP(=O)(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 8PI "SYSTEMATIC NAME" ACDLabs 12.01 "1-{[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]amino}-1,2-dideoxy-5-O-phosphono-D-erythro-pentitol" 8PI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S})-5-[(2-azanyl-5-formamido-6-oxidanylidene-5~{H}-pyrimidin-4-yl)amino]-2,3-bis(oxidanyl)pentyl] 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 8PI "Create component" 2021-09-23 RCSB 8PI "Initial release" 2022-08-03 RCSB #