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 ?
#