data_N9X
# 
_chem_comp.id                                    N9X 
_chem_comp.name                                  Ertapenem 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H27 N3 O7 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(3~{R},4~{R},5~{S})-3-[(3~{S},5~{R})-5-[(4-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-4-methyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]pyrrolidine-2-carboxylic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-08-16 
_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                        477.531 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     N9X 
_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        8AKM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
N9X N1  N1  N 0 1 N N N N N N 19.293 4.379  18.555 1.216  2.379  1.686  N1  N9X 1  
N9X C2  C1  C 0 1 N N R N N N 17.996 8.657  20.853 -3.199 0.968  0.547  C2  N9X 2  
N9X O2  O1  O 0 1 N N N N N N 19.462 10.474 18.958 -4.161 3.284  -1.008 O2  N9X 3  
N9X C4  C2  C 0 1 N N N N N N 19.743 6.072  20.248 0.871  1.454  -0.532 C4  N9X 4  
N9X C5  C3  C 0 1 N N R N N N 19.981 4.611  19.833 1.863  2.217  0.366  C5  N9X 5  
N9X C6  C4  C 0 1 N N N N N N 21.480 4.343  19.710 3.137  1.425  0.512  C6  N9X 6  
N9X N   N2  N 0 1 N N N N N N 22.093 4.877  18.656 4.072  1.467  -0.458 N   N9X 7  
N9X C   C5  C 0 1 N N N N N N 16.786 7.245  22.604 -2.490 -1.298 -0.353 C   N9X 8  
N9X O   O2  O 0 1 N N N N N N 22.060 3.678  20.573 3.321  0.750  1.503  O   N9X 9  
N9X C1  C6  C 0 1 N N R N N N 17.290 8.628  22.220 -3.151 -0.557 0.811  C1  N9X 10 
N9X C10 C7  C 0 1 N N S N N N 16.204 9.705  22.085 -4.660 -0.885 0.897  C10 N9X 11 
N9X C11 C8  C 0 1 N N S N N N 14.789 9.273  21.653 -4.945 -2.247 0.262  C11 N9X 12 
N9X C12 C9  C 0 1 N N N N N N 14.299 10.330 20.714 -4.705 -2.170 -1.224 C12 N9X 13 
N9X C13 C10 C 0 1 N N R N N N 13.718 9.183  22.739 -6.401 -2.637 0.523  C13 N9X 14 
N9X C14 C11 C 0 1 N N N N N N 12.424 8.591  22.221 -6.686 -4.000 -0.111 C14 N9X 15 
N9X C3  C12 C 0 1 N N S N N N 19.000 6.769  19.019 -0.378 1.226  0.349  C3  N9X 16 
N9X C7  C13 C 0 1 N N N N N N 18.794 5.626  18.014 -0.246 2.329  1.430  C7  N9X 17 
N9X C8  C14 C 0 1 N N N N N N 17.646 10.051 20.404 -4.567 1.185  -0.060 C8  N9X 18 
N9X C9  C15 C 0 1 N N N N N N 18.298 10.706 19.238 -4.973 2.408  -0.793 C9  N9X 19 
N9X N2  N3  N 0 1 N N N N N N 16.707 10.634 21.055 -5.325 0.182  0.140  N2  N9X 20 
N9X O1  O3  O 0 1 N N N N N N 17.550 11.531 18.555 -6.242 2.547  -1.220 O1  N9X 21 
N9X O3  O4  O 0 1 N N N N N N 13.943 10.146 19.574 -3.877 -2.882 -1.739 O3  N9X 22 
N9X O4  O5  O 0 1 N N N N N N 14.244 8.402  23.811 -6.629 -2.711 1.932  O4  N9X 23 
N9X S   S1  S 0 1 N N N N N N 17.416 7.418  19.638 -1.896 1.454  -0.618 S   N9X 24 
N9X H12 H1  H 0 1 N N N N N N 18.526 3.754  18.703 1.479  3.256  2.112  H12 N9X 25 
N9X H3  H3  H 0 1 N N N N N N 19.083 8.529  20.966 -3.102 1.521  1.481  H3  N9X 26 
N9X H10 H4  H 0 1 N N N N N N 20.702 6.573  20.448 0.614  2.053  -1.406 H10 N9X 27 
N9X H9  H5  H 0 1 N N N N N N 19.113 6.115  21.149 1.298  0.499  -0.840 H9  N9X 28 
N9X H11 H6  H 0 1 N N N N N N 19.562 3.950  20.606 2.078  3.195  -0.065 H11 N9X 29 
N9X H2  H7  H 0 1 N N N N N N 22.993 5.298  18.541 3.955  2.059  -1.218 H2  N9X 30 
N9X H8  H9  H 0 1 N N N N N N 16.294 7.293  23.587 -1.439 -1.016 -0.414 H8  N9X 31 
N9X H7  H10 H 0 1 N N N N N N 16.066 6.895  21.850 -2.569 -2.373 -0.191 H7  N9X 32 
N9X H6  H11 H 0 1 N N N N N N 17.634 6.546  22.653 -2.992 -1.034 -1.284 H6  N9X 33 
N9X H   H12 H 0 1 N N N N N N 18.009 8.959  22.984 -2.645 -0.778 1.751  H   N9X 34 
N9X H4  H13 H 0 1 N N N N N N 16.124 10.239 23.044 -4.991 -0.875 1.935  H4  N9X 35 
N9X H16 H14 H 0 1 N N N N N N 14.853 8.310  21.126 -4.285 -2.997 0.698  H16 N9X 36 
N9X H22 H15 H 0 1 N N N N N N 14.260 11.343 21.087 -5.272 -1.477 -1.827 H22 N9X 37 
N9X H5  H16 H 0 1 N N N N N N 13.510 10.202 23.098 -7.062 -1.888 0.087  H5  N9X 38 
N9X H19 H17 H 0 1 N N N N N N 11.688 8.547  23.037 -6.026 -4.749 0.325  H19 N9X 39 
N9X H20 H18 H 0 1 N N N N N N 12.033 9.220  21.408 -7.724 -4.277 0.075  H20 N9X 40 
N9X H18 H19 H 0 1 N N N N N N 12.611 7.576  21.842 -6.512 -3.943 -1.186 H18 N9X 41 
N9X H1  H20 H 0 1 N N N N N N 19.589 7.599  18.603 -0.356 0.234  0.801  H1  N9X 42 
N9X H14 H21 H 0 1 N N N N N N 19.334 5.859  17.085 -0.785 2.047  2.334  H14 N9X 43 
N9X H13 H22 H 0 1 N N N N N N 17.720 5.523  17.798 -0.603 3.285  1.049  H13 N9X 44 
N9X H15 H26 H 0 1 N N N N N N 18.054 11.897 17.838 -6.459 3.362  -1.694 H15 N9X 45 
N9X H21 H27 H 0 1 N N N N N N 13.594 8.332  24.501 -6.074 -3.359 2.387  H21 N9X 46 
N9X C15 C16 C 0 1 Y N N N N N ?      ?      ?      5.205  0.661  -0.369 C15 N9X 47 
N9X C16 C17 C 0 1 Y N N N N N ?      ?      ?      5.774  0.397  0.873  C16 N9X 48 
N9X C17 C22 C 0 1 Y N N N N N ?      ?      ?      6.893  -0.398 0.965  C17 N9X 49 
N9X C18 C18 C 0 1 Y N N N N N ?      ?      ?      7.459  -0.942 -0.192 C18 N9X 50 
N9X C19 C19 C 0 1 Y N N N N N ?      ?      ?      6.885  -0.675 -1.439 C19 N9X 51 
N9X C20 C20 C 0 1 Y N N N N N ?      ?      ?      5.763  0.117  -1.522 C20 N9X 52 
N9X C21 C21 C 0 1 N N N N N N ?      ?      ?      8.658  -1.795 -0.098 C21 N9X 53 
N9X O5  O6  O 0 1 N N N N N N ?      ?      ?      9.156  -2.026 0.986  O5  N9X 54 
N9X O6  O7  O 0 1 N N N N N N ?      ?      ?      9.202  -2.318 -1.214 O6  N9X 55 
N9X H17 H25 H 0 1 N N N N N N ?      ?      ?      5.336  0.818  1.767  H17 N9X 56 
N9X H25 H30 H 0 1 N N N N N N ?      ?      ?      7.334  -0.603 1.930  H25 N9X 57 
N9X H26 H31 H 0 1 N N N N N N ?      ?      ?      7.320  -1.093 -2.335 H26 N9X 58 
N9X H27 H28 H 0 1 N N N N N N ?      ?      ?      5.319  0.324  -2.485 H27 N9X 59 
N9X H28 H29 H 0 1 N N N N N N ?      ?      ?      9.988  -2.871 -1.102 H28 N9X 60 
# 
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 
N9X C7  N1  SING N N 1  
N9X C7  C3  SING N N 2  
N9X N1  C5  SING N N 3  
N9X O1  C9  SING N N 4  
N9X N   C6  SING N N 5  
N9X O2  C9  DOUB N N 6  
N9X C3  S   SING N N 7  
N9X C3  C4  SING N N 8  
N9X C9  C8  SING N N 9  
N9X O3  C12 DOUB N N 10 
N9X S   C2  SING N N 11 
N9X C6  C5  SING N N 12 
N9X C6  O   DOUB N N 13 
N9X C5  C4  SING N N 14 
N9X C8  C2  SING N N 15 
N9X C8  N2  DOUB N N 16 
N9X C12 C11 SING N N 17 
N9X C2  C1  SING N N 18 
N9X N2  C10 SING N N 19 
N9X C11 C10 SING N N 20 
N9X C11 C13 SING N N 21 
N9X C10 C1  SING N N 22 
N9X C1  C   SING N N 23 
N9X C14 C13 SING N N 24 
N9X C13 O4  SING N N 25 
N9X N1  H12 SING N N 26 
N9X C2  H3  SING N N 27 
N9X C4  H10 SING N N 28 
N9X C4  H9  SING N N 29 
N9X C5  H11 SING N N 30 
N9X N   H2  SING N N 31 
N9X C   H8  SING N N 32 
N9X C   H7  SING N N 33 
N9X C   H6  SING N N 34 
N9X C1  H   SING N N 35 
N9X C10 H4  SING N N 36 
N9X C11 H16 SING N N 37 
N9X C12 H22 SING N N 38 
N9X C13 H5  SING N N 39 
N9X C14 H19 SING N N 40 
N9X C14 H20 SING N N 41 
N9X C14 H18 SING N N 42 
N9X C3  H1  SING N N 43 
N9X C7  H14 SING N N 44 
N9X C7  H13 SING N N 45 
N9X O1  H15 SING N N 46 
N9X O4  H21 SING N N 47 
N9X N   C15 SING N N 48 
N9X C15 C16 SING Y N 49 
N9X C16 C17 DOUB Y N 50 
N9X C17 C18 SING Y N 51 
N9X C18 C19 DOUB Y N 52 
N9X C19 C20 SING Y N 53 
N9X C20 C15 DOUB Y N 54 
N9X C18 C21 SING N N 55 
N9X C21 O5  DOUB N N 56 
N9X C21 O6  SING N N 57 
N9X C16 H17 SING N N 58 
N9X C17 H25 SING N N 59 
N9X C19 H26 SING N N 60 
N9X C20 H27 SING N N 61 
N9X O6  H28 SING N N 62 
# 
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 
N9X InChI            InChI                1.06    "InChI=1S/C22H27N3O7S/c1-10-17(15(9-26)11(2)27)25-18(22(31)32)19(10)33-14-7-16(23-8-14)20(28)24-13-5-3-12(4-6-13)21(29)30/h3-6,9-11,14-17,19,23,27H,7-8H2,1-2H3,(H,24,28)(H,29,30)(H,31,32)/t10-,11-,14+,15-,16-,17-,19-/m1/s1" 
N9X InChIKey         InChI                1.06    AKERAHWFSYYFHP-OIROVCEBSA-N                                                                                                                                                                                                     
N9X SMILES_CANONICAL CACTVS               3.385   "C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@H](S[C@@H]2CN[C@H](C2)C(=O)Nc3ccc(cc3)C(O)=O)[C@@H]1C)C(O)=O"                                                                                                                               
N9X SMILES           CACTVS               3.385   "C[CH](O)[CH](C=O)[CH]1N=C([CH](S[CH]2CN[CH](C2)C(=O)Nc3ccc(cc3)C(O)=O)[CH]1C)C(O)=O"                                                                                                                                           
N9X SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@H]1[C@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=O)O)S[C@H]2C[C@@H](NC2)C(=O)Nc3ccc(cc3)C(=O)O"                                                                                                                                  
N9X SMILES           "OpenEye OEToolkits" 3.1.0.0 "CC1C(C(=NC1C(C=O)C(C)O)C(=O)O)SC2CC(NC2)C(=O)Nc3ccc(cc3)C(=O)O"                                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           N9X 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   3.1.0.0 
_pdbx_chem_comp_identifier.identifier        "(2~{S},3~{R},4~{R})-4-[(3~{S},5~{R})-5-[(4-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      N9X 
_pdbx_chem_comp_synonyms.name         "(3~{R},4~{R},5~{S})-3-[(3~{S},5~{R})-5-[(4-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-4-methyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]pyrrolidine-2-carboxylic acid" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
N9X "Create component"     2022-08-16 PDBE 
N9X "Modify aromatic_flag" 2022-10-05 PDBE 
N9X "Other modification"   2022-10-06 PDBE 
N9X "Other modification"   2022-10-13 PDBE 
N9X "Initial release"      2023-03-08 RCSB 
N9X "Modify PCM"           2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            N9X 
_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               C12 
_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      ? 
# 
