data_RPD # _chem_comp.id RPD _chem_comp.name "(C8-R)-HYDANTOCIDIN 5'-PHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H22 N3 O13 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 459.300 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RPD _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 1QF4 _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 RPD O1P O1P O 0 1 N N N 25.212 11.748 23.784 -1.348 -1.066 -6.653 O1P RPD 1 RPD O2P O2P O 0 1 N N N 27.238 12.877 23.098 -2.179 1.269 -7.129 O2P RPD 2 RPD O3P O3P O 0 1 N N N 25.068 13.594 22.275 0.320 0.588 -7.575 O3P RPD 3 RPD P P P 0 1 N N N 25.780 13.051 23.420 -0.953 0.359 -6.617 P RPD 4 RPD "O5'" O5* O 0 1 N N N 25.668 14.053 24.698 -0.571 0.773 -5.109 "O5'" RPD 5 RPD "C5'" C5* C 0 1 N N N 26.240 13.795 25.957 0.517 -0.064 -4.714 "C5'" RPD 6 RPD "C4'" C4* C 0 1 N N R 27.053 14.986 26.437 0.931 0.278 -3.281 "C4'" RPD 7 RPD "O4'" O4* O 0 1 N N N 28.289 15.046 25.744 -0.160 0.041 -2.375 "O4'" RPD 8 RPD "C3'" C3* C 0 1 N N S 26.386 16.320 26.203 2.065 -0.664 -2.806 "C3'" RPD 9 RPD "O3'" O3* O 0 1 N N N 26.806 17.253 27.211 3.347 -0.155 -3.177 "O3'" RPD 10 RPD "C2'" C2* C 0 1 N N R 26.958 16.747 24.805 1.866 -0.615 -1.265 "C2'" RPD 11 RPD "O2'" O2* O 0 1 N N N 27.106 18.181 24.778 2.535 0.514 -0.701 "O2'" RPD 12 RPD "C1'" C1* C 0 1 N N S 28.351 16.074 24.691 0.341 -0.468 -1.143 "C1'" RPD 13 RPD N1 N1 N 0 1 N N N 28.402 15.432 23.483 -0.276 -1.752 -0.801 N1 RPD 14 RPD C2 C2 C 0 1 N N N 29.507 15.838 22.756 -0.889 -1.573 0.385 C2 RPD 15 RPD O2 O2 O 0 1 N N N 29.787 15.439 21.686 -1.506 -2.445 0.965 O2 RPD 16 RPD N3 N3 N 0 1 N N N 30.213 16.769 23.473 -0.742 -0.327 0.852 N3 RPD 17 RPD C4 C4 C 0 1 N N N 29.513 16.936 24.675 -0.018 0.437 0.008 C4 RPD 18 RPD O4 O4 O 0 1 N N N 29.909 17.731 25.542 0.284 1.602 0.149 O4 RPD 19 RPD C5A C5A C 0 1 N N N 31.454 17.447 23.039 -1.303 0.147 2.120 C5A RPD 20 RPD C6A C6A C 0 1 N N N 31.148 18.892 22.595 -0.291 -0.084 3.244 C6A RPD 21 RPD C7A C7A C 0 1 N N N 30.001 18.931 21.555 -0.876 0.411 4.567 C7A RPD 22 RPD C8A C8A C 0 1 N N R 29.778 20.402 21.112 0.168 0.263 5.675 C8A RPD 23 RPD C9A C9A C 0 1 N N N 28.331 20.655 20.700 0.458 -1.197 5.899 C9A RPD 24 RPD OJA O91A O 0 1 N N N 27.308 20.036 21.332 -0.160 -1.860 6.888 OJA RPD 25 RPD OKA O92A O 0 1 N N N 28.087 21.519 19.685 1.248 -1.773 5.188 OKA RPD 26 RPD NAA N10A N 0 1 N N N 30.623 20.798 19.931 -0.346 0.857 6.916 NAA RPD 27 RPD OAA O10A O 0 1 N N N 31.419 21.964 20.297 -1.705 0.345 7.095 OAA RPD 28 RPD CBA C11A C 0 1 N N N 31.514 19.716 19.497 -0.466 2.301 6.675 CBA RPD 29 RPD OBA O11A O 0 1 N N N 32.302 20.114 18.379 0.816 2.838 6.349 OBA RPD 30 RPD HO2P HO2P H 0 0 N N N 27.605 13.720 22.862 -2.375 0.990 -8.034 HO2P RPD 31 RPD HO3P HO3P H 0 0 N N N 25.435 14.437 22.039 0.545 1.527 -7.523 HO3P RPD 32 RPD "H5'1" 1H5* H 0 0 N N N 25.470 13.493 26.705 1.361 0.096 -5.384 "H5'1" RPD 33 RPD "H5'2" 2H5* H 0 0 N N N 26.845 12.858 25.950 0.207 -1.108 -4.762 "H5'2" RPD 34 RPD H4 H4 H 0 1 N N N 27.173 14.823 27.533 1.253 1.318 -3.220 H4 RPD 35 RPD H3 H3 H 0 1 N N N 25.272 16.281 26.237 1.921 -1.675 -3.188 H3 RPD 36 RPD "HO3'" HO3* H 0 0 N N N 26.386 18.092 27.063 3.362 -0.112 -4.143 "HO3'" RPD 37 RPD H2 H2 H 0 1 N N N 26.289 16.443 23.965 2.207 -1.540 -0.799 H2 RPD 38 RPD "HO2'" HO2* H 0 0 N N N 27.452 18.439 23.931 3.477 0.405 -0.892 "HO2'" RPD 39 RPD HN1 HN1 H 0 1 N N N 27.537 15.552 22.954 -0.249 -2.569 -1.325 HN1 RPD 40 RPD H51 1H5 H 0 1 N N N 32.243 17.412 23.825 -2.221 -0.397 2.338 H51 RPD 41 RPD H52 2H5 H 0 1 N N N 31.986 16.872 22.245 -1.522 1.212 2.043 H52 RPD 42 RPD H61 1H6 H 0 1 N N N 30.931 19.550 23.468 0.626 0.460 3.025 H61 RPD 43 RPD H62 2H6 H 0 1 N N N 32.062 19.405 22.215 -0.071 -1.149 3.320 H62 RPD 44 RPD H71 1H7 H 0 1 N N N 30.185 18.249 20.692 -1.758 -0.177 4.818 H71 RPD 45 RPD H72 2H7 H 0 1 N N N 29.066 18.453 21.932 -1.156 1.460 4.470 H72 RPD 46 RPD H81 1H8 H 0 1 N N N 30.060 21.004 22.006 1.084 0.775 5.380 H81 RPD 47 RPD H91 H91 H 0 1 N N N 26.407 20.193 21.075 0.026 -2.798 7.032 H91 RPD 48 RPD H10 H10 H 0 1 N N N 31.952 22.213 19.551 -1.628 -0.607 7.240 H10 RPD 49 RPD H111 1H11 H 0 0 N N N 32.149 19.347 20.335 -0.846 2.788 7.573 H111 RPD 50 RPD H112 2H11 H 0 0 N N N 30.948 18.778 19.286 -1.154 2.475 5.848 H112 RPD 51 RPD H11 H11 H 0 1 N N N 32.878 19.413 18.098 0.693 3.785 6.199 H11 RPD 52 # # 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 RPD O1P P DOUB N N 1 RPD O2P P SING N N 2 RPD O2P HO2P SING N N 3 RPD O3P P SING N N 4 RPD O3P HO3P SING N N 5 RPD P "O5'" SING N N 6 RPD "O5'" "C5'" SING N N 7 RPD "C5'" "C4'" SING N N 8 RPD "C5'" "H5'1" SING N N 9 RPD "C5'" "H5'2" SING N N 10 RPD "C4'" "O4'" SING N N 11 RPD "C4'" "C3'" SING N N 12 RPD "C4'" H4 SING N N 13 RPD "O4'" "C1'" SING N N 14 RPD "C3'" "O3'" SING N N 15 RPD "C3'" "C2'" SING N N 16 RPD "C3'" H3 SING N N 17 RPD "O3'" "HO3'" SING N N 18 RPD "C2'" "O2'" SING N N 19 RPD "C2'" "C1'" SING N N 20 RPD "C2'" H2 SING N N 21 RPD "O2'" "HO2'" SING N N 22 RPD "C1'" N1 SING N N 23 RPD "C1'" C4 SING N N 24 RPD N1 C2 SING N N 25 RPD N1 HN1 SING N N 26 RPD C2 O2 DOUB N N 27 RPD C2 N3 SING N N 28 RPD N3 C4 SING N N 29 RPD N3 C5A SING N N 30 RPD C4 O4 DOUB N N 31 RPD C5A C6A SING N N 32 RPD C5A H51 SING N N 33 RPD C5A H52 SING N N 34 RPD C6A C7A SING N N 35 RPD C6A H61 SING N N 36 RPD C6A H62 SING N N 37 RPD C7A C8A SING N N 38 RPD C7A H71 SING N N 39 RPD C7A H72 SING N N 40 RPD C8A C9A SING N N 41 RPD C8A NAA SING N N 42 RPD C8A H81 SING N N 43 RPD C9A OJA SING N N 44 RPD C9A OKA DOUB N N 45 RPD OJA H91 SING N N 46 RPD NAA OAA SING N N 47 RPD NAA CBA SING N N 48 RPD OAA H10 SING N N 49 RPD CBA OBA SING N N 50 RPD CBA H111 SING N N 51 RPD CBA H112 SING N N 52 RPD OBA H11 SING N N 53 # # 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 RPD SMILES ACDLabs 10.04 "O=C(O)C(N(O)CO)CCCN2C(=O)C1(OC(C(O)C1O)COP(=O)(O)O)NC2=O" RPD SMILES_CANONICAL CACTVS 3.341 "OCN(O)[C@H](CCCN1C(=O)N[C@@]2(O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O" RPD SMILES CACTVS 3.341 "OCN(O)[CH](CCCN1C(=O)N[C]2(O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O" RPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(C[C@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)NC1=O" RPD SMILES "OpenEye OEToolkits" 1.5.0 "C(CC(C(=O)O)N(CO)O)CN1C(=O)C2(C(C(C(O2)COP(=O)(O)O)O)O)NC1=O" RPD InChI InChI 1.03 "InChI=1S/C13H22N3O13P/c17-5-16(24)6(10(20)21)2-1-3-15-11(22)13(14-12(15)23)9(19)8(18)7(29-13)4-28-30(25,26)27/h6-9,17-19,24H,1-5H2,(H,14,23)(H,20,21)(H2,25,26,27)/t6-,7-,8-,9-,13+/m1/s1" RPD InChIKey InChI 1.03 MAXSFYCTFIBEAR-OJMIUMIFSA-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 RPD "SYSTEMATIC NAME" ACDLabs 10.04 "5-{(5S,7R,8S,9R)-8,9-dihydroxy-2,4-dioxo-7-[(phosphonooxy)methyl]-6-oxa-1,3-diazaspiro[4.4]non-3-yl}-N-hydroxy-N-(hydroxymethyl)-D-norvaline" RPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-5-[(2R,3S,4R,5S)-3,4-dihydroxy-7,9-dioxo-2-(phosphonooxymethyl)-1-oxa-6,8-diazaspiro[4.4]nonan-8-yl]-2-(hydroxy-(hydroxymethyl)amino)pentanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RPD "Create component" 1999-07-08 RCSB RPD "Modify descriptor" 2011-06-04 RCSB RPD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RPD _pdbx_chem_comp_synonyms.name "[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##