data_5S4 # _chem_comp.id 5S4 _chem_comp.name "[(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate" _chem_comp.type PEPTIDE-LIKE _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H33 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-11-19 _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 440.429 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5ES8 _chem_comp.pdbx_subcomponent_list "2JD BAL EDN VAL" _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 5S4 C10 C1 C 0 1 N N N N N N -117.305 111.931 27.782 2.729 1.841 0.045 C16 2JD 1 5S4 O27 O6 O 0 1 N N N N N N -118.026 111.556 26.873 2.652 2.522 1.046 O3 2JD 2 5S4 C08 C11 C 0 1 N N R N N N -116.406 113.109 27.564 4.075 1.556 -0.570 C17 2JD 3 5S4 O09 O3 O 0 1 N N N N N N -116.910 113.890 26.516 3.894 0.981 -1.866 O4 2JD 4 5S4 C05 C8 C 0 1 N N N N N N -114.998 112.620 27.173 4.845 0.578 0.319 C18 2JD 5 5S4 C04 C7 C 0 1 N N N N N N -115.140 111.659 25.989 6.147 0.173 -0.377 C19 2JD 6 5S4 C06 C9 C 0 1 N N N N N N -114.123 113.835 26.755 5.169 1.249 1.655 C20 2JD 7 5S4 C07 C10 C 0 1 N N N N N N -114.341 111.905 28.339 3.991 -0.667 0.567 C21 2JD 8 5S4 P02 P1 P 0 1 N N N N N N -113.135 110.220 25.248 8.286 -1.375 0.035 P 2JD 9 5S4 O03 O2 O 0 1 N N N N N N -113.902 111.606 25.296 6.866 -0.741 0.454 O2P 2JD 10 5S4 O01 O1 O 0 1 N N N N N N -113.236 109.519 26.584 9.237 -0.287 -0.286 O3P 2JD 11 5S4 O29 O7 O 0 1 N N N N N N -113.715 109.344 24.167 8.863 -2.251 1.256 OXT 2JD 12 5S4 N11 N1 N 0 1 N N N N N N -117.305 111.253 29.075 1.612 1.335 -0.513 N BAL 13 5S4 C12 C12 C 0 1 N N N N N N -118.144 110.120 29.353 0.317 1.512 0.149 CB BAL 14 5S4 C13 C2 C 0 1 N N N N N N -119.615 110.495 29.134 -0.779 0.847 -0.687 CA BAL 15 5S4 C14 C13 C 0 1 N N N N N N -120.731 109.705 29.889 -2.110 1.029 -0.006 C BAL 16 5S4 O26 O5 O 0 1 N N N N N N -121.899 109.953 29.648 -2.177 1.631 1.045 O BAL 17 5S4 N18 N3 N 0 1 N N N N N N -121.705 108.368 33.990 -6.913 0.212 -0.076 NAA EDN 18 5S4 C17 C3 C 0 1 N N N N N N -121.950 108.920 32.673 -5.618 0.035 -0.738 CAB EDN 19 5S4 C16 C14 C 0 1 N N N N N N -121.461 107.992 31.561 -4.522 0.700 0.098 CAC EDN 20 5S4 N15 N2 N 0 1 N N N N N N -120.385 108.699 30.859 -3.228 0.523 -0.564 NAD EDN 21 5S4 N24 N4 N 0 1 N N N N N N -124.844 108.663 34.244 -10.442 -0.303 -0.931 N VAL 22 5S4 C20 C4 C 0 1 N N S N N N -123.832 109.563 34.640 -9.362 -0.112 0.047 CA VAL 23 5S4 C19 C15 C 0 1 N N N N N N -122.645 108.693 35.020 -8.030 -0.294 -0.635 C VAL 24 5S4 O25 O4 O 0 1 N N N N N N -122.530 108.269 36.142 -7.964 -0.896 -1.686 O VAL 25 5S4 C21 C5 C 0 1 N N N N N N -124.352 110.388 35.796 -9.504 -1.140 1.171 CB VAL 26 5S4 C22 C6 C 0 1 N N N N N N -125.576 111.155 35.375 -10.856 -0.956 1.863 CG1 VAL 27 5S4 C23 C16 C 0 1 N N N N N N -123.312 111.363 36.351 -9.419 -2.551 0.585 CG2 VAL 28 5S4 H19 H19 H 0 1 N N N N N N -116.336 113.695 28.492 4.637 2.485 -0.661 H15 2JD 29 5S4 H20 H20 H 0 1 N N N N N N -117.613 113.422 26.081 3.400 0.149 -1.862 H16 2JD 30 5S4 H11 H11 H 0 1 N N N N N N -115.928 112.020 25.312 5.916 -0.305 -1.329 H17 2JD 31 5S4 H21 H21 H 0 1 N N N N N N -116.698 111.590 29.795 1.665 0.854 -1.354 H BAL 32 5S4 H23 H23 H 0 1 N N N N N N -117.999 109.806 30.397 0.349 1.052 1.137 HB3 BAL 33 5S4 H22 H22 H 0 1 N N N N N N -117.874 109.292 28.680 0.103 2.576 0.250 HB2 BAL 34 5S4 H1 H1 H 0 1 N N N N N N -119.722 111.552 29.420 -0.810 1.306 -1.675 HA1 BAL 35 5S4 H2 H2 H 0 1 N N N N N N -119.817 110.384 28.058 -0.564 -0.217 -0.788 HA2 BAL 36 5S4 H27 H27 H 0 1 N N N N N N -120.913 107.785 34.172 -6.966 0.693 0.765 HAA2 EDN 37 5S4 H3 H3 H 0 1 N N N N N N -121.425 109.883 32.588 -5.403 -1.028 -0.839 HAB1 EDN 38 5S4 H4 H4 H 0 1 N N N N N N -123.031 109.081 32.551 -5.650 0.495 -1.727 HAB2 EDN 39 5S4 H25 H25 H 0 1 N N N N N N -122.284 107.769 30.866 -4.737 1.764 0.198 HAC1 EDN 40 5S4 H26 H26 H 0 1 N N N N N N -121.080 107.054 31.991 -4.491 0.241 1.086 HAC2 EDN 41 5S4 H24 H24 H 0 1 N N N N N N -119.427 108.486 31.051 -3.175 0.042 -1.405 HAD2 EDN 42 5S4 H31 H31 H 0 1 N N N N N N -125.661 109.175 33.979 -10.407 -1.228 -1.332 H VAL 43 5S4 H32 H32 H 0 1 N N N N N N -124.523 108.122 33.467 -11.343 -0.123 -0.513 H2 VAL 44 5S4 H5 H5 H 0 1 N N N N N N -123.549 110.228 33.811 -9.422 0.893 0.464 HA VAL 45 5S4 H6 H6 H 0 1 N N N N N N -124.638 109.701 36.606 -8.703 -0.999 1.896 HB VAL 46 5S4 H7 H7 H 0 1 N N N N N N -125.945 111.751 36.223 -11.658 -1.097 1.137 HG11 VAL 47 5S4 H8 H8 H 0 1 N N N N N N -125.320 111.824 34.540 -10.958 -1.688 2.664 HG12 VAL 48 5S4 H9 H9 H 0 1 N N N N N N -126.358 110.451 35.054 -10.917 0.050 2.280 HG13 VAL 49 5S4 H28 H28 H 0 1 N N N N N N -123.749 111.931 37.185 -8.456 -2.683 0.093 HG21 VAL 50 5S4 H29 H29 H 0 1 N N N N N N -122.437 110.801 36.709 -9.521 -3.284 1.386 HG22 VAL 51 5S4 H30 H30 H 0 1 N N N N N N -123.001 112.059 35.557 -10.220 -2.693 -0.140 HG23 VAL 52 5S4 OP3 OP3 O 0 1 N Y N N N N ? ? ? 8.092 -2.316 -1.257 OP3 5S4 53 5S4 H10 H10 H 0 1 N N N N N N -115.402 110.656 26.356 6.755 1.060 -0.554 H10 5S4 54 5S4 H12 H12 H 0 1 N N N N N N -114.022 114.525 27.606 4.242 1.467 2.186 H12 5S4 55 5S4 H13 H13 H 0 1 N N N N N N -113.127 113.482 26.449 5.784 0.581 2.258 H13 5S4 56 5S4 H14 H14 H 0 1 N N N N N N -114.601 114.359 25.914 5.710 2.178 1.473 H14 5S4 57 5S4 H15 H15 H 0 1 N N N N N N -114.241 112.599 29.186 3.761 -1.145 -0.385 H15 5S4 58 5S4 H16 H16 H 0 1 N N N N N N -114.961 111.047 28.639 4.540 -1.364 1.200 H16 5S4 59 5S4 H17 H17 H 0 1 N N N N N N -113.345 111.550 28.037 3.064 -0.379 1.062 H17 5S4 60 5S4 H18 H18 H 0 1 N N N N N N -114.025 108.531 24.549 9.719 -2.664 1.073 H18 5S4 61 5S4 H33 H33 H 0 1 N Y N N N N ? ? ? 7.481 -3.053 -1.119 H33 5S4 62 # 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 5S4 O29 P02 SING N N 1 5S4 P02 O03 SING N N 2 5S4 P02 O01 DOUB N N 3 5S4 O03 C04 SING N N 4 5S4 C04 C05 SING N N 5 5S4 O09 C08 SING N N 6 5S4 C06 C05 SING N N 7 5S4 O27 C10 DOUB N N 8 5S4 C05 C08 SING N N 9 5S4 C05 C07 SING N N 10 5S4 C08 C10 SING N N 11 5S4 C10 N11 SING N N 12 5S4 N11 C12 SING N N 13 5S4 C13 C12 SING N N 14 5S4 C13 C14 SING N N 15 5S4 O26 C14 DOUB N N 16 5S4 C14 N15 SING N N 17 5S4 N15 C16 SING N N 18 5S4 C16 C17 SING N N 19 5S4 C17 N18 SING N N 20 5S4 N18 C19 SING N N 21 5S4 N24 C20 SING N N 22 5S4 C20 C19 SING N N 23 5S4 C20 C21 SING N N 24 5S4 C19 O25 DOUB N N 25 5S4 C22 C21 SING N N 26 5S4 C21 C23 SING N N 27 5S4 C13 H1 SING N N 28 5S4 C13 H2 SING N N 29 5S4 C17 H3 SING N N 30 5S4 C17 H4 SING N N 31 5S4 C20 H5 SING N N 32 5S4 C21 H6 SING N N 33 5S4 C22 H7 SING N N 34 5S4 C22 H8 SING N N 35 5S4 C22 H9 SING N N 36 5S4 C04 H11 SING N N 37 5S4 C08 H19 SING N N 38 5S4 O09 H20 SING N N 39 5S4 N11 H21 SING N N 40 5S4 C12 H22 SING N N 41 5S4 C12 H23 SING N N 42 5S4 N15 H24 SING N N 43 5S4 C16 H25 SING N N 44 5S4 C16 H26 SING N N 45 5S4 N18 H27 SING N N 46 5S4 C23 H28 SING N N 47 5S4 C23 H29 SING N N 48 5S4 C23 H30 SING N N 49 5S4 N24 H31 SING N N 50 5S4 N24 H32 SING N N 51 5S4 P02 OP3 SING N N 52 5S4 C04 H10 SING N N 53 5S4 C06 H12 SING N N 54 5S4 C06 H13 SING N N 55 5S4 C06 H14 SING N N 56 5S4 C07 H15 SING N N 57 5S4 C07 H16 SING N N 58 5S4 C07 H17 SING N N 59 5S4 O29 H18 SING N N 60 5S4 OP3 H33 SING N N 61 # 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 5S4 InChI InChI 1.03 "InChI=1S/C16H33N4O8P/c1-10(2)12(17)14(23)20-8-7-18-11(21)5-6-19-15(24)13(22)16(3,4)9-28-29(25,26)27/h10,12-13,22H,5-9,17H2,1-4H3,(H,18,21)(H,19,24)(H,20,23)(H2,25,26,27)/t12-,13-/m0/s1" 5S4 InChIKey InChI 1.03 MFHZIFARQCIIMR-STQMWFEESA-N 5S4 SMILES_CANONICAL CACTVS 3.385 "CC(C)[C@H](N)C(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O" 5S4 SMILES CACTVS 3.385 "CC(C)[CH](N)C(=O)NCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O" 5S4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CC(C)[C@@H](C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)N" 5S4 SMILES "OpenEye OEToolkits" 2.0.4 "CC(C)C(C(=O)NCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O)N" # _pdbx_chem_comp_identifier.comp_id 5S4 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.4 _pdbx_chem_comp_identifier.identifier "[(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] 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 5S4 "Create component" 2015-11-19 RCSB 5S4 "Initial release" 2016-01-20 RCSB 5S4 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 5S4 _pdbx_chem_comp_pcm.modified_residue_id SER _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _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 P02 _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 ? #