data_RPL # _chem_comp.id RPL _chem_comp.name "(C8-S)-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 RPL _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 1QF5 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 RPL O1P O1P O 0 1 N N N 25.211 11.844 23.912 -1.247 -1.215 -6.727 O1P RPL 1 RPL O2P O2P O 0 1 N N N 27.226 12.761 23.016 -2.096 1.086 -7.322 O2P RPL 2 RPL O3P O3P O 0 1 N N N 25.075 13.557 22.283 0.420 0.420 -7.682 O3P RPL 3 RPL P P P 0 1 N N N 25.821 13.064 23.420 -0.871 0.216 -6.744 P RPL 4 RPL "O5'" O5* O 0 1 N N N 25.865 14.142 24.627 -0.529 0.698 -5.246 "O5'" RPL 5 RPL "C5'" C5* C 0 1 N N N 26.327 13.849 25.929 0.559 -0.106 -4.792 "C5'" RPL 6 RPL "C4'" C4* C 0 1 N N R 27.168 14.993 26.493 0.936 0.303 -3.366 "C4'" RPL 7 RPL "O4'" O4* O 0 1 N N N 28.421 15.070 25.825 -0.173 0.089 -2.476 "O4'" RPL 8 RPL "C3'" C3* C 0 1 N N S 26.551 16.360 26.292 2.070 -0.604 -2.826 "C3'" RPL 9 RPL "O3'" O3* O 0 1 N N N 27.136 17.312 27.188 3.355 -0.093 -3.190 "O3'" RPL 10 RPL "C2'" C2* C 0 1 N N R 27.005 16.659 24.840 1.836 -0.491 -1.293 "C2'" RPL 11 RPL "O2'" O2* O 0 1 N N N 27.032 18.071 24.662 2.478 0.670 -0.763 "O2'" RPL 12 RPL "C1'" C1* C 0 1 N N S 28.445 16.075 24.746 0.307 -0.359 -1.212 "C1'" RPL 13 RPL N1 N1 N 0 1 N N N 28.553 15.453 23.541 -0.302 -1.636 -0.829 N1 RPL 14 RPL C2 C2 C 0 1 N N N 29.616 15.959 22.824 -0.944 -1.415 0.334 C2 RPL 15 RPL O2 O2 O 0 1 N N N 29.926 15.583 21.746 -1.564 -2.270 0.938 O2 RPL 16 RPL N3 N3 N 0 1 N N N 30.237 16.947 23.576 -0.824 -0.149 0.751 N3 RPL 17 RPL C4 C4 C 0 1 N N N 29.521 17.028 24.752 -0.090 0.589 -0.108 C4 RPL 18 RPL O4 O4 O 0 1 N N N 29.846 17.834 25.621 0.194 1.763 -0.011 O4 RPL 19 RPL C5A C5A C 0 1 N N N 31.408 17.767 23.214 -1.419 0.372 1.984 C5A RPL 20 RPL C6A C6A C 0 1 N N N 31.169 18.457 21.862 -0.431 0.202 3.139 C6A RPL 21 RPL C7A C7A C 0 1 N N N 30.027 19.502 21.947 -1.052 0.746 4.427 C7A RPL 22 RPL C8A C8A C 0 1 N N S 29.578 19.916 20.510 -0.064 0.576 5.582 C8A RPL 23 RPL C9A C9A C 0 1 N N N 28.270 20.708 20.548 -0.676 1.112 6.850 C9A RPL 24 RPL OJA O91A O 0 1 N N N 27.969 21.523 19.517 -1.396 0.303 7.643 OJA RPL 25 RPL OKA O92A O 0 1 N N N 27.430 20.618 21.597 -0.519 2.271 7.154 OKA RPL 26 RPL NAA N10A N 0 1 N N N 30.598 20.799 19.817 0.246 -0.849 5.754 NAA RPL 27 RPL OAA O10A O 0 1 N N N 31.157 21.760 20.765 -0.987 -1.499 6.194 OAA RPL 28 RPL CBA C11A C 0 1 N N N 31.679 19.999 19.237 1.195 -0.942 6.872 CBA RPL 29 RPL OBA O11A O 0 1 N N N 32.385 20.720 18.230 2.374 -0.198 6.560 OBA RPL 30 RPL HO2P HO2P H 0 0 N N N 27.625 13.560 22.693 -2.269 0.766 -8.218 HO2P RPL 31 RPL HO3P HO3P H 0 0 N N N 25.474 14.356 21.960 0.632 1.363 -7.665 HO3P RPL 32 RPL "H5'1" 1H5* H 0 0 N N N 25.485 13.585 26.611 1.416 0.036 -5.449 "H5'1" RPL 33 RPL "H5'2" 2H5* H 0 0 N N N 26.881 12.881 25.957 0.264 -1.155 -4.802 "H5'2" RPL 34 RPL H4 H4 H 0 1 N N N 27.254 14.759 27.579 1.244 1.348 -3.343 H4 RPL 35 RPL H3 H3 H 0 1 N N N 25.451 16.405 26.468 1.948 -1.631 -3.167 H3 RPL 36 RPL "HO3'" HO3* H 0 0 N N N 26.748 18.170 27.061 3.391 -0.091 -4.156 "HO3'" RPL 37 RPL H2 H2 H 0 1 N N N 26.333 16.221 24.065 2.177 -1.390 -0.780 H2 RPL 38 RPL "HO2'" HO2* H 0 0 N N N 27.310 18.254 23.772 3.425 0.566 -0.928 "HO2'" RPL 39 RPL HN1 HN1 H 0 1 N N N 27.682 15.501 23.011 -0.253 -2.474 -1.316 HN1 RPL 40 RPL H51 1H5 H 0 1 N N N 31.670 18.496 24.014 -2.335 -0.175 2.205 H51 RPL 41 RPL H52 2H5 H 0 1 N N N 32.351 17.173 23.219 -1.650 1.430 1.856 H52 RPL 42 RPL H61 1H6 H 0 1 N N N 32.107 18.910 21.465 0.484 0.750 2.918 H61 RPL 43 RPL H62 2H6 H 0 1 N N N 30.980 17.713 21.053 -0.200 -0.855 3.267 H62 RPL 44 RPL H71 1H7 H 0 1 N N N 29.172 19.139 22.564 -1.968 0.198 4.648 H71 RPL 45 RPL H72 2H7 H 0 1 N N N 30.311 20.383 22.567 -1.284 1.804 4.299 H72 RPL 46 RPL H81 1H8 H 0 1 N N N 29.457 18.959 19.950 0.851 1.124 5.361 H81 RPL 47 RPL H91 H91 H 0 1 N N N 27.156 22.014 19.540 -1.789 0.647 8.457 H91 RPL 48 RPL H10 H10 H 0 1 N N N 31.795 22.313 20.330 -1.612 -1.438 5.459 H10 RPL 49 RPL H111 1H11 H 0 0 N N N 32.370 19.617 20.024 1.458 -1.986 7.039 H111 RPL 50 RPL H112 2H11 H 0 0 N N N 31.301 19.024 18.850 0.735 -0.534 7.773 H112 RPL 51 RPL H11 H11 H 0 1 N N N 33.086 20.201 17.853 2.968 -0.285 7.318 H11 RPL 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 RPL O1P P DOUB N N 1 RPL O2P P SING N N 2 RPL O2P HO2P SING N N 3 RPL O3P P SING N N 4 RPL O3P HO3P SING N N 5 RPL P "O5'" SING N N 6 RPL "O5'" "C5'" SING N N 7 RPL "C5'" "C4'" SING N N 8 RPL "C5'" "H5'1" SING N N 9 RPL "C5'" "H5'2" SING N N 10 RPL "C4'" "O4'" SING N N 11 RPL "C4'" "C3'" SING N N 12 RPL "C4'" H4 SING N N 13 RPL "O4'" "C1'" SING N N 14 RPL "C3'" "O3'" SING N N 15 RPL "C3'" "C2'" SING N N 16 RPL "C3'" H3 SING N N 17 RPL "O3'" "HO3'" SING N N 18 RPL "C2'" "O2'" SING N N 19 RPL "C2'" "C1'" SING N N 20 RPL "C2'" H2 SING N N 21 RPL "O2'" "HO2'" SING N N 22 RPL "C1'" N1 SING N N 23 RPL "C1'" C4 SING N N 24 RPL N1 C2 SING N N 25 RPL N1 HN1 SING N N 26 RPL C2 O2 DOUB N N 27 RPL C2 N3 SING N N 28 RPL N3 C4 SING N N 29 RPL N3 C5A SING N N 30 RPL C4 O4 DOUB N N 31 RPL C5A C6A SING N N 32 RPL C5A H51 SING N N 33 RPL C5A H52 SING N N 34 RPL C6A C7A SING N N 35 RPL C6A H61 SING N N 36 RPL C6A H62 SING N N 37 RPL C7A C8A SING N N 38 RPL C7A H71 SING N N 39 RPL C7A H72 SING N N 40 RPL C8A C9A SING N N 41 RPL C8A NAA SING N N 42 RPL C8A H81 SING N N 43 RPL C9A OJA SING N N 44 RPL C9A OKA DOUB N N 45 RPL OJA H91 SING N N 46 RPL NAA OAA SING N N 47 RPL NAA CBA SING N N 48 RPL OAA H10 SING N N 49 RPL CBA OBA SING N N 50 RPL CBA H111 SING N N 51 RPL CBA H112 SING N N 52 RPL 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 RPL SMILES ACDLabs 10.04 "O=C(O)C(N(O)CO)CCCN2C(=O)C1(OC(C(O)C1O)COP(=O)(O)O)NC2=O" RPL 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" RPL 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" RPL 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" RPL 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" RPL 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-/m0/s1" RPL InChIKey InChI 1.03 MAXSFYCTFIBEAR-FUIMDIGMSA-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 RPL "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)-L-norvaline" RPL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-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 RPL "Create component" 1999-07-08 EBI RPL "Modify descriptor" 2011-06-04 RCSB RPL "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RPL _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 ? ##