data_PM5 # _chem_comp.id PM5 _chem_comp.name "S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) HEPTANETHIOATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H35 N2 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-12-19 _chem_comp.pdbx_modified_date 2024-09-27 _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 454.518 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PM5 _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 2FAD _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 PM5 O23 O23 O 0 1 N N N N N N 10.967 28.588 25.576 7.521 4.120 0.032 O23 PM5 1 PM5 P24 P24 P 0 1 N N S N N N 10.570 28.044 24.186 6.874 2.819 0.725 P24 PM5 2 PM5 O26 O26 O 0 1 N N N N N N 9.525 26.928 24.349 5.567 3.177 1.321 O26 PM5 3 PM5 O27 O27 O 0 1 N N N N N N 9.952 29.206 23.376 6.662 1.670 -0.382 O27 PM5 4 PM5 C28 C28 C 0 1 N N N N N N 9.420 29.161 22.057 6.404 0.305 -0.047 C28 PM5 5 PM5 C29 C29 C 0 1 N N N N N N 8.776 30.517 21.684 6.254 -0.515 -1.330 C29 PM5 6 PM5 C30 C30 C 0 1 N N N N N N 7.784 30.250 20.544 5.090 0.036 -2.156 C30 PM5 7 PM5 C31 C31 C 0 1 N N N N N N 8.002 31.045 22.904 7.546 -0.426 -2.146 C31 PM5 8 PM5 C32 C32 C 0 1 N N R N N N 9.839 31.552 21.225 5.978 -1.977 -0.972 C32 PM5 9 PM5 O33 O33 O 0 1 N N N N N N 10.504 31.048 20.063 7.121 -2.531 -0.317 O33 PM5 10 PM5 C34 C34 C 0 1 N N N N N N 9.137 32.884 20.882 4.786 -2.052 -0.052 C34 PM5 11 PM5 O35 O35 O 0 1 N N N N N N 8.530 33.512 21.755 4.932 -2.394 1.103 O35 PM5 12 PM5 N36 N36 N 0 1 N N N N N N 9.223 33.317 19.620 3.559 -1.739 -0.512 N36 PM5 13 PM5 C37 C37 C 0 1 N N N N N N 8.601 34.557 19.146 2.416 -1.718 0.405 C37 PM5 14 PM5 C38 C38 C 0 1 N N N N N N 8.998 35.009 17.731 1.151 -1.335 -0.366 C38 PM5 15 PM5 C39 C39 C 0 1 N N N N N N 10.472 35.337 17.545 -0.024 -1.314 0.577 C39 PM5 16 PM5 O40 O40 O 0 1 N N N N N N 11.283 34.457 17.273 0.134 -1.578 1.750 O40 PM5 17 PM5 N41 N41 N 0 1 N N N N N N 10.767 36.633 17.700 -1.252 -1.001 0.116 N41 PM5 18 PM5 C42 C42 C 0 1 N N N N N N 12.076 37.300 17.590 -2.394 -0.979 1.033 C42 PM5 19 PM5 C43 C43 C 0 1 N N N N N N 12.407 37.655 16.137 -3.659 -0.597 0.262 C43 PM5 20 PM5 S1 S1 S 0 1 N N N N N N 13.943 38.601 15.760 -5.071 -0.571 1.395 S1 PM5 21 PM5 C1 C1 C 0 1 N N N N N N 13.637 40.174 16.585 -6.317 -0.129 0.307 C1 PM5 22 PM5 O1 O1 O 0 1 N N N N N N 12.596 40.349 17.176 -6.061 0.060 -0.864 O1 PM5 23 PM5 C2 C2 C 0 1 N N N N N N 14.684 41.282 16.538 -7.731 0.025 0.803 C2 PM5 24 PM5 C3 C3 C 0 1 N N N N N N 14.371 42.371 15.508 -8.640 0.423 -0.361 C3 PM5 25 PM5 C4 C4 C 0 1 N N N N N N 15.361 43.546 15.614 -10.076 0.580 0.143 C4 PM5 26 PM5 C5 C5 C 0 1 N N N N N N 15.718 43.911 17.065 -10.985 0.977 -1.022 C5 PM5 27 PM5 C6 C6 C 0 1 N N N N N N 16.746 45.041 17.156 -12.421 1.134 -0.518 C6 PM5 28 PM5 C7 C7 C 0 1 N N N N N N 17.828 44.913 16.102 -13.330 1.531 -1.683 C7 PM5 29 PM5 H23 H23 H 0 1 N N N N N N 11.049 27.866 26.188 7.677 4.854 0.641 H23 PM5 30 PM5 H24 H24 H 0 1 N N N N N N 11.709 27.520 23.519 7.744 2.343 1.742 H24 PM5 31 PM5 H281 1H28 H 0 0 N N N N N N 8.650 28.377 22.011 7.233 -0.088 0.541 H281 PM5 32 PM5 H282 2H28 H 0 0 N N N N N N 10.232 28.941 21.349 5.484 0.241 0.534 H282 PM5 33 PM5 H301 1H30 H 0 0 N N N N N N 8.041 29.302 20.049 5.337 1.038 -2.507 H301 PM5 34 PM5 H302 2H30 H 0 0 N N N N N N 7.836 31.071 19.813 4.911 -0.615 -3.011 H302 PM5 35 PM5 H303 3H30 H 0 0 N N N N N N 6.764 30.186 20.952 4.194 0.079 -1.537 H303 PM5 36 PM5 H311 1H31 H 0 0 N N N N N N 7.215 30.327 23.177 8.364 -0.874 -1.582 H311 PM5 37 PM5 H312 2H31 H 0 0 N N N N N N 7.545 32.014 22.657 7.418 -0.960 -3.088 H312 PM5 38 PM5 H313 3H31 H 0 0 N N N N N N 8.693 31.171 23.751 7.775 0.620 -2.349 H313 PM5 39 PM5 H32 H32 H 0 1 N N N N N N 10.572 31.722 22.028 5.771 -2.541 -1.881 H32 PM5 40 PM5 H33 H33 H 0 1 N N N N N N 9.874 30.936 19.361 7.363 -2.078 0.502 H33 PM5 41 PM5 H36 H36 H 0 1 N N N N N N 9.739 32.766 18.965 3.432 -1.528 -1.450 H36 PM5 42 PM5 H371 1H37 H 0 0 N N N N N N 8.951 35.349 19.825 2.288 -2.705 0.847 H371 PM5 43 PM5 H372 2H37 H 0 0 N N N N N N 7.512 34.400 19.148 2.596 -0.987 1.193 H372 PM5 44 PM5 H381 1H38 H 0 0 N N N N N N 8.448 35.942 17.540 1.280 -0.348 -0.809 H381 PM5 45 PM5 H382 2H38 H 0 0 N N N N N N 8.749 34.191 17.039 0.971 -2.066 -1.155 H382 PM5 46 PM5 H41 H41 H 0 1 N N N N N N 9.995 37.229 17.920 -1.378 -0.789 -0.822 H41 PM5 47 PM5 H421 1H42 H 0 0 N N N N N N 12.848 36.610 17.961 -2.523 -1.967 1.476 H421 PM5 48 PM5 H422 2H42 H 0 0 N N N N N N 12.053 38.225 18.184 -2.214 -0.249 1.821 H422 PM5 49 PM5 H431 1H43 H 0 0 N N N N N N 11.597 38.338 15.841 -3.531 0.390 -0.181 H431 PM5 50 PM5 H432 2H43 H 0 0 N N N N N N 12.494 36.700 15.599 -3.839 -1.328 -0.526 H432 PM5 51 PM5 H21 1H2 H 0 1 N N N N N N 15.637 40.819 16.244 -8.073 -0.919 1.225 H21 PM5 52 PM5 H22 2H2 H 0 1 N N N N N N 14.731 41.752 17.531 -7.765 0.799 1.571 H22 PM5 53 PM5 H31 1H3 H 0 1 N N N N N N 13.358 42.752 15.703 -8.298 1.368 -0.783 H31 PM5 54 PM5 H32A 2H3 H 0 0 N N N N N N 14.442 41.937 14.500 -8.607 -0.351 -1.129 H32A PM5 55 PM5 H41A 1H4 H 0 0 N N N N N N 14.876 44.425 15.164 -10.418 -0.365 0.565 H41A PM5 56 PM5 H42 2H4 H 0 1 N N N N N N 16.287 43.263 15.093 -10.109 1.353 0.910 H42 PM5 57 PM5 H51 1H5 H 0 1 N N N N N N 16.160 43.020 17.534 -10.643 1.922 -1.444 H51 PM5 58 PM5 H52 2H5 H 0 1 N N N N N N 14.800 44.235 17.577 -10.952 0.203 -1.789 H52 PM5 59 PM5 H61 1H6 H 0 1 N N N N N N 17.225 44.986 18.144 -12.763 0.189 -0.096 H61 PM5 60 PM5 H62 2H6 H 0 1 N N N N N N 16.227 46.000 17.012 -12.455 1.907 0.249 H62 PM5 61 PM5 H71 1H7 H 0 1 N N N N N N 18.397 43.987 16.272 -14.353 1.643 -1.324 H71 PM5 62 PM5 H72 2H7 H 0 1 N N N N N N 18.506 45.777 16.166 -12.988 2.476 -2.105 H72 PM5 63 PM5 H73 3H7 H 0 1 N N N N N N 17.367 44.882 15.104 -13.297 0.757 -2.450 H73 PM5 64 # 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 PM5 O23 P24 SING N N 1 PM5 O23 H23 SING N N 2 PM5 P24 O26 DOUB N N 3 PM5 P24 O27 SING N N 4 PM5 P24 H24 SING N N 5 PM5 O27 C28 SING N N 6 PM5 C28 C29 SING N N 7 PM5 C28 H281 SING N N 8 PM5 C28 H282 SING N N 9 PM5 C29 C30 SING N N 10 PM5 C29 C31 SING N N 11 PM5 C29 C32 SING N N 12 PM5 C30 H301 SING N N 13 PM5 C30 H302 SING N N 14 PM5 C30 H303 SING N N 15 PM5 C31 H311 SING N N 16 PM5 C31 H312 SING N N 17 PM5 C31 H313 SING N N 18 PM5 C32 O33 SING N N 19 PM5 C32 C34 SING N N 20 PM5 C32 H32 SING N N 21 PM5 O33 H33 SING N N 22 PM5 C34 O35 DOUB N N 23 PM5 C34 N36 SING N N 24 PM5 N36 C37 SING N N 25 PM5 N36 H36 SING N N 26 PM5 C37 C38 SING N N 27 PM5 C37 H371 SING N N 28 PM5 C37 H372 SING N N 29 PM5 C38 C39 SING N N 30 PM5 C38 H381 SING N N 31 PM5 C38 H382 SING N N 32 PM5 C39 O40 DOUB N N 33 PM5 C39 N41 SING N N 34 PM5 N41 C42 SING N N 35 PM5 N41 H41 SING N N 36 PM5 C42 C43 SING N N 37 PM5 C42 H421 SING N N 38 PM5 C42 H422 SING N N 39 PM5 C43 S1 SING N N 40 PM5 C43 H431 SING N N 41 PM5 C43 H432 SING N N 42 PM5 S1 C1 SING N N 43 PM5 C1 O1 DOUB N N 44 PM5 C1 C2 SING N N 45 PM5 C2 C3 SING N N 46 PM5 C2 H21 SING N N 47 PM5 C2 H22 SING N N 48 PM5 C3 C4 SING N N 49 PM5 C3 H31 SING N N 50 PM5 C3 H32A SING N N 51 PM5 C4 C5 SING N N 52 PM5 C4 H41A SING N N 53 PM5 C4 H42 SING N N 54 PM5 C5 C6 SING N N 55 PM5 C5 H51 SING N N 56 PM5 C5 H52 SING N N 57 PM5 C6 C7 SING N N 58 PM5 C6 H61 SING N N 59 PM5 C6 H62 SING N N 60 PM5 C7 H71 SING N N 61 PM5 C7 H72 SING N N 62 PM5 C7 H73 SING N N 63 # 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 PM5 SMILES ACDLabs 10.04 "O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)O)CCCCCC" PM5 InChI InChI 1.03 "InChI=1S/C18H35N2O7PS/c1-4-5-6-7-8-15(22)29-12-11-19-14(21)9-10-20-17(24)16(23)18(2,3)13-27-28(25)26/h16,23,28H,4-13H2,1-3H3,(H,19,21)(H,20,24)(H,25,26)/t16-/m0/s1" PM5 InChIKey InChI 1.03 IPSBILXXAVXCDA-INIZCTEOSA-N PM5 SMILES_CANONICAL CACTVS 3.385 "CCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[PH](O)=O" PM5 SMILES CACTVS 3.385 "CCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[PH](O)=O" PM5 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "CCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@H](=O)O)O" PM5 SMILES "OpenEye OEToolkits" 1.7.5 "CCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=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 PM5 "SYSTEMATIC NAME" ACDLabs 10.04 "S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxido)phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] heptanethioate" PM5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R)-4-[[3-(2-heptanoylsulfanylethylamino)-3-oxo-propyl]amino]-3-hydroxy-2,2-dimethyl-4-oxo-butoxy]phosphinic 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 PM5 "Create component" 2005-12-19 RCSB PM5 "Modify descriptor" 2011-06-04 RCSB PM5 "Modify descriptor" 2012-01-05 RCSB PM5 "Modify coordinates" 2012-01-05 RCSB PM5 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id PM5 _pdbx_chem_comp_pcm.modified_residue_id SER _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Lipid/lipid-like _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom P24 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #