data_YMD # _chem_comp.id YMD _chem_comp.name "(1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H39 N3 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-12 _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 505.625 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YMD _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 7LZX _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 YMD C02 C1 C 0 1 N N N N N N 11.287 24.038 25.682 2.427 -0.130 0.014 C02 YMD 1 YMD C04 C2 C 0 1 N N S N N N 12.281 22.070 26.913 0.072 0.081 0.600 C04 YMD 2 YMD C05 C3 C 0 1 N N N N N N 13.388 21.813 27.926 -0.032 1.434 1.306 C05 YMD 3 YMD C06 C4 C 0 1 N N N N N N 14.739 22.280 27.404 1.236 1.681 2.126 C06 YMD 4 YMD C07 C5 C 0 1 N N N N N N 15.124 21.515 26.145 1.187 3.085 2.731 C07 YMD 5 YMD C08 C6 C 0 1 N N N N N N 15.815 22.159 28.478 1.327 0.644 3.248 C08 YMD 6 YMD C09 C7 C 0 1 N N N N N N 10.963 21.576 27.482 -1.225 -0.217 -0.108 C09 YMD 7 YMD C11 C8 C 0 1 N N S N N N 9.119 19.881 27.404 -3.647 -0.484 -0.103 C11 YMD 8 YMD C12 C9 C 0 1 N N N N N N 8.018 19.892 26.309 -3.852 0.663 -1.096 C12 YMD 9 YMD C13 C10 C 0 1 N N S N N N 7.750 21.185 25.694 -3.955 1.985 -0.333 C13 YMD 10 YMD C14 C11 C 0 1 N N N N N N 6.699 21.026 24.503 -4.149 3.137 -1.294 C14 YMD 11 YMD C16 C12 C 0 1 N N N N N N 6.034 22.712 26.034 -5.667 3.482 0.429 C16 YMD 12 YMD C17 C13 C 0 1 N N N N N N 7.049 22.065 26.699 -5.228 2.005 0.544 C17 YMD 13 YMD C19 C14 C 0 1 N N R N N N 9.303 18.502 28.036 -3.632 -1.815 -0.858 C19 YMD 14 YMD C23 C15 C 0 1 N N N N N N 10.288 25.925 24.700 4.766 -0.380 -0.392 C23 YMD 15 YMD C24 C16 C 0 1 N N N N N N 8.883 26.063 25.279 5.594 -1.023 -1.506 C24 YMD 16 YMD C25 C17 C 0 1 N N N N N N 7.947 26.802 24.330 7.003 -1.320 -0.988 C25 YMD 17 YMD C26 C18 C 0 1 N N N N N N 8.507 28.155 23.900 7.669 -0.016 -0.544 C26 YMD 18 YMD C27 C19 C 0 1 N N N N N N 7.596 28.724 22.822 9.077 -0.313 -0.026 C27 YMD 19 YMD C28 C20 C 0 1 N N N N N N 8.495 29.123 25.083 7.755 0.943 -1.734 C28 YMD 20 YMD C29 C21 C 0 1 N N N N N N 9.920 28.042 23.340 6.840 0.627 0.570 C29 YMD 21 YMD C30 C22 C 0 1 N N N N N N 10.856 27.275 24.268 5.432 0.925 0.051 C30 YMD 22 YMD N03 N1 N 0 1 N N N N N N 12.194 23.488 26.657 1.163 0.123 -0.377 N03 YMD 23 YMD N10 N2 N 0 1 N N N N N N 10.376 20.398 26.897 -2.372 -0.304 0.595 N10 YMD 24 YMD N15 N3 N 0 1 N N N N N N 5.714 21.911 24.713 -5.115 3.956 -0.846 N15 YMD 25 YMD O01 O1 O 0 1 N N N N N N 10.698 23.350 24.925 2.663 -0.392 1.177 O01 YMD 26 YMD O18 O2 O 0 1 N N N N N N 6.771 20.287 23.601 -3.522 3.298 -2.320 O18 YMD 27 YMD O20 O3 O 0 1 N N N N N N 10.126 18.679 29.160 -4.868 -1.982 -1.555 O20 YMD 28 YMD O21 O4 O 0 1 N N N N N N 10.422 22.151 28.361 -1.237 -0.379 -1.310 O21 YMD 29 YMD O22 O5 O 0 1 N N N N N N 11.136 25.421 25.674 3.429 -0.097 -0.885 O22 YMD 30 YMD H1 H1 H 0 1 N N N N N N 12.504 21.525 25.984 0.272 -0.698 1.335 H1 YMD 31 YMD H2 H2 H 0 1 N N N N N N 13.156 22.355 28.854 -0.144 2.224 0.563 H2 YMD 32 YMD H3 H3 H 0 1 N N N N N N 13.439 20.734 28.135 -0.899 1.433 1.968 H3 YMD 33 YMD H4 H4 H 0 1 N N N N N N 14.648 23.343 27.137 2.109 1.594 1.479 H4 YMD 34 YMD H5 H5 H 0 1 N N N N N N 16.102 21.868 25.786 0.314 3.172 3.378 H5 YMD 35 YMD H6 H6 H 0 1 N N N N N N 15.183 20.440 26.373 2.091 3.260 3.315 H6 YMD 36 YMD H7 H7 H 0 1 N N N N N N 14.365 21.684 25.367 1.122 3.823 1.932 H7 YMD 37 YMD H8 H8 H 0 1 N N N N N N 15.507 22.721 29.372 2.230 0.820 3.832 H8 YMD 38 YMD H9 H9 H 0 1 N N N N N N 15.953 21.100 28.741 0.454 0.731 3.894 H9 YMD 39 YMD H10 H10 H 0 1 N N N N N N 16.762 22.568 28.096 1.361 -0.356 2.817 H10 YMD 40 YMD H11 H11 H 0 1 N N N N N N 8.775 20.555 28.202 -4.461 -0.486 0.622 H11 YMD 41 YMD H12 H12 H 0 1 N N N N N N 7.083 19.535 26.766 -3.006 0.704 -1.782 H12 YMD 42 YMD H13 H13 H 0 1 N N N N N N 8.326 19.197 25.514 -4.769 0.495 -1.660 H13 YMD 43 YMD H14 H14 H 0 1 N N N N N N 8.669 21.662 25.322 -3.067 2.141 0.279 H14 YMD 44 YMD H15 H15 H 0 1 N N N N N N 6.349 23.735 25.781 -6.754 3.553 0.420 H15 YMD 45 YMD H16 H16 H 0 1 N N N N N N 5.138 22.751 26.671 -5.258 4.062 1.257 H16 YMD 46 YMD H17 H17 H 0 1 N N N N N N 6.635 21.452 27.513 -5.991 1.340 0.140 H17 YMD 47 YMD H18 H18 H 0 1 N N N N N N 7.755 22.799 27.115 -4.995 1.747 1.577 H18 YMD 48 YMD S1 S1 S 0 1 N Y N N N N 9.751 17.823 27.341 -3.414 -3.176 0.322 S1 YMD 49 YMD H20 H20 H 0 1 N N N N N N 8.310 18.186 28.389 -2.809 -1.818 -1.572 H20 YMD 50 YMD H21 H21 H 0 1 N N N N N N 10.251 25.257 23.827 4.704 -1.062 0.455 H21 YMD 51 YMD H22 H22 H 0 1 N N N N N N 8.942 26.620 26.226 5.120 -1.952 -1.822 H22 YMD 52 YMD H23 H23 H 0 1 N N N N N N 8.476 25.059 25.469 5.656 -0.340 -2.354 H23 YMD 53 YMD H24 H24 H 0 1 N N N N N N 6.984 26.963 24.837 6.941 -2.003 -0.140 H24 YMD 54 YMD H25 H25 H 0 1 N N N N N N 7.791 26.183 23.434 7.593 -1.778 -1.781 H25 YMD 55 YMD H26 H26 H 0 1 N N N N N N 6.572 28.810 23.215 9.667 -0.771 -0.819 H26 YMD 56 YMD H27 H27 H 0 1 N N N N N N 7.959 29.718 22.523 9.552 0.616 0.290 H27 YMD 57 YMD H28 H28 H 0 1 N N N N N N 7.599 28.055 21.949 9.016 -0.996 0.822 H28 YMD 58 YMD H29 H29 H 0 1 N N N N N N 9.147 28.737 25.880 6.752 1.155 -2.103 H29 YMD 59 YMD H30 H30 H 0 1 N N N N N N 8.861 30.107 24.755 8.230 1.872 -1.418 H30 YMD 60 YMD H31 H31 H 0 1 N N N N N N 7.468 29.222 25.465 8.345 0.485 -2.527 H31 YMD 61 YMD H32 H32 H 0 1 N N N N N N 9.876 27.519 22.373 6.779 -0.055 1.417 H32 YMD 62 YMD H33 H33 H 0 1 N N N N N N 10.323 29.055 23.191 7.315 1.556 0.885 H33 YMD 63 YMD H34 H34 H 0 1 N N N N N N 11.808 27.104 23.744 5.493 1.607 -0.797 H34 YMD 64 YMD H35 H35 H 0 1 N N N N N N 11.036 27.884 25.166 4.842 1.383 0.844 H35 YMD 65 YMD H36 H36 H 0 1 N N N N N N 12.783 24.109 27.174 0.975 0.332 -1.305 H36 YMD 66 YMD H37 H37 H 0 1 N N N N N N 10.836 19.935 26.139 -2.353 -0.247 1.563 H37 YMD 67 YMD H38 H38 H 0 1 N N N N N N 4.912 22.041 24.130 -5.411 4.757 -1.306 H38 YMD 68 YMD H39 H39 H 0 1 N N N N N N 10.267 17.841 29.585 -5.051 -1.288 -2.204 H39 YMD 69 YMD O1 O6 O 0 1 N Y N N N N ? ? ? -4.342 -3.062 1.392 O1 YMD 70 YMD O2 O7 O 0 1 N Y N N N N ? ? ? -3.236 -4.407 -0.365 O2 YMD 71 YMD O3 O8 O 0 1 N Y N N N N ? ? ? -2.062 -2.907 0.967 O3 YMD 72 YMD H19 H19 H 0 1 N Y N N N N ? ? ? -1.806 -3.562 1.630 H19 YMD 73 # 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 YMD C27 C26 SING N N 1 YMD C29 C26 SING N N 2 YMD C29 C30 SING N N 3 YMD O18 C14 DOUB N N 4 YMD C26 C25 SING N N 5 YMD C26 C28 SING N N 6 YMD C30 C23 SING N N 7 YMD C25 C24 SING N N 8 YMD C14 N15 SING N N 9 YMD C14 C13 SING N N 10 YMD C23 C24 SING N N 11 YMD C23 O22 SING N N 12 YMD N15 C16 SING N N 13 YMD O01 C02 DOUB N N 14 YMD O22 C02 SING N N 15 YMD C02 N03 SING N N 16 YMD C13 C12 SING N N 17 YMD C13 C17 SING N N 18 YMD C16 C17 SING N N 19 YMD C07 C06 SING N N 20 YMD C12 C11 SING N N 21 YMD N03 C04 SING N N 22 YMD N10 C11 SING N N 23 YMD N10 C09 SING N N 24 YMD C04 C09 SING N N 25 YMD C04 C05 SING N N 26 YMD C11 C19 SING N N 27 YMD C06 C05 SING N N 28 YMD C06 C08 SING N N 29 YMD C09 O21 DOUB N N 30 YMD C19 O20 SING N N 31 YMD C04 H1 SING N N 32 YMD C05 H2 SING N N 33 YMD C05 H3 SING N N 34 YMD C06 H4 SING N N 35 YMD C07 H5 SING N N 36 YMD C07 H6 SING N N 37 YMD C07 H7 SING N N 38 YMD C08 H8 SING N N 39 YMD C08 H9 SING N N 40 YMD C08 H10 SING N N 41 YMD C11 H11 SING N N 42 YMD C12 H12 SING N N 43 YMD C12 H13 SING N N 44 YMD C13 H14 SING N N 45 YMD C16 H15 SING N N 46 YMD C16 H16 SING N N 47 YMD C17 H17 SING N N 48 YMD C17 H18 SING N N 49 YMD C19 S1 SING N N 50 YMD C19 H20 SING N N 51 YMD C23 H21 SING N N 52 YMD C24 H22 SING N N 53 YMD C24 H23 SING N N 54 YMD C25 H24 SING N N 55 YMD C25 H25 SING N N 56 YMD C27 H26 SING N N 57 YMD C27 H27 SING N N 58 YMD C27 H28 SING N N 59 YMD C28 H29 SING N N 60 YMD C28 H30 SING N N 61 YMD C28 H31 SING N N 62 YMD C29 H32 SING N N 63 YMD C29 H33 SING N N 64 YMD C30 H34 SING N N 65 YMD C30 H35 SING N N 66 YMD N03 H36 SING N N 67 YMD N10 H37 SING N N 68 YMD N15 H38 SING N N 69 YMD O20 H39 SING N N 70 YMD S1 O1 DOUB N N 71 YMD S1 O2 DOUB N N 72 YMD S1 O3 SING N N 73 YMD O3 H19 SING N N 74 # 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 YMD SMILES ACDLabs 12.01 "CC(C)CC(NC(=O)OC1CCC(C)(C)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O" YMD InChI InChI 1.03 "InChI=1S/C22H39N3O8S/c1-13(2)11-16(25-21(29)33-15-5-8-22(3,4)9-6-15)19(27)24-17(20(28)34(30,31)32)12-14-7-10-23-18(14)26/h13-17,20,28H,5-12H2,1-4H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t14-,16-,17-,20+/m0/s1" YMD InChIKey InChI 1.03 LGCFVMZACNBZBJ-JWWIWJDOSA-N YMD SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O" YMD SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O" YMD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)(C)C" YMD SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)(C)C" # 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 YMD "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2S)-2-[(N-{[(4,4-dimethylcyclohexyl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid" YMD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-2-[(4,4-dimethylcyclohexyl)oxycarbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic 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 YMD "Create component" 2021-03-12 RCSB YMD "Initial release" 2021-03-24 RCSB YMD "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YMD _pdbx_chem_comp_pcm.modified_residue_id CYS _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 C19 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #