data_O2F
#
_chem_comp.id O2F
_chem_comp.name "(2S,3R,4R)-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H27 N3 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Meropenem, bound form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-08-26
_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 385.478
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code O2F
_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 8AKL
_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
O2F C1 C1 C 0 1 N N N N N N 17.134 3.943 19.743 7.483 -0.589 -0.970 C1 O2F 1
O2F C2 C2 C 0 1 N N N N N N 17.339 3.610 22.196 5.631 -2.320 -0.850 C2 O2F 2
O2F C3 C3 C 0 1 N N S N N N 20.020 4.747 19.756 4.058 -0.579 0.740 C3 O2F 3
O2F C4 C4 C 0 1 N N N N N N 18.937 5.931 17.959 2.147 0.522 1.680 C4 O2F 4
O2F C5 C5 C 0 1 N N N N N N 20.088 6.249 20.085 3.008 -0.405 -0.386 C5 O2F 5
O2F C7 C6 C 0 1 N N R N N N 18.225 8.653 21.109 -0.946 0.759 0.637 C7 O2F 6
O2F C9 C7 C 0 1 N N N N N N 18.439 10.750 19.507 -1.857 2.924 -0.586 C9 O2F 7
O2F C11 C8 C 0 1 N N S N N N 14.963 9.370 21.772 -3.943 -1.303 0.159 C11 O2F 8
O2F C15 C9 C 0 1 N N R N N N 17.443 8.649 22.453 -1.592 -0.639 0.800 C15 O2F 9
O2F C16 C10 C 0 1 N N N N N N 16.948 7.265 22.888 -1.311 -1.522 -0.417 C16 O2F 10
O2F N N1 N 0 1 N N N N N N 18.011 3.844 20.915 6.157 -0.998 -0.500 N O2F 11
O2F C C11 C 0 1 N N N N N N 19.356 3.950 20.885 5.422 -0.159 0.255 C O2F 12
O2F O O1 O 0 1 N N N N N N 20.055 3.451 21.747 5.857 0.936 0.545 O O2F 13
O2F C10 C12 C 0 1 N N S N N N 16.360 9.775 22.320 -3.089 -0.258 0.881 C10 O2F 14
O2F C12 C13 C 0 1 N N N N N N 14.390 10.442 20.885 -3.662 -1.245 -1.321 C12 O2F 15
O2F C13 C14 C 0 1 N N R N N N 13.927 9.326 22.892 -5.424 -1.013 0.409 C13 O2F 16
O2F C14 C15 C 0 1 N N N N N N 12.626 8.694 22.449 -6.277 -2.058 -0.313 C14 O2F 17
O2F C6 C16 C 0 1 N N S N N N 19.142 6.963 19.090 1.696 -0.261 0.429 C6 O2F 18
O2F C8 C17 C 0 1 N N N N N N 17.883 10.061 20.680 -2.058 1.606 0.060 C8 O2F 19
O2F N1 N2 N 0 1 N N N N N N 19.309 4.583 18.480 3.599 0.313 1.825 N1 O2F 20
O2F N2 N3 N 0 1 N N N N N N 16.939 10.670 21.292 -3.190 1.039 0.202 N2 O2F 21
O2F O1 O2 O 0 1 N N N N N N 19.661 10.418 19.213 -2.921 3.646 -0.988 O1 O2F 22
O2F O2 O3 O 0 1 N N N N N N 17.805 11.567 18.926 -0.734 3.353 -0.754 O2 O2F 23
O2F O3 O4 O 0 1 N N N N N N 14.025 10.228 19.708 -3.232 -2.218 -1.893 O3 O2F 24
O2F O4 O5 O 0 1 N N N N N N 14.465 8.600 24.007 -5.690 -1.068 1.811 O4 O2F 25
O2F S S1 S 0 1 N N N N N N 17.582 7.458 19.860 0.460 0.681 -0.507 S O2F 26
O2F H7 H1 H 0 1 N N N N N N 16.087 3.820 20.056 7.923 -1.393 -1.561 H7 O2F 27
O2F H8 H2 H 0 1 N N N N N N 17.262 4.929 19.272 7.390 0.305 -1.586 H8 O2F 28
O2F H6 H3 H 0 1 N N N N N N 17.396 3.155 19.022 8.123 -0.376 -0.114 H6 O2F 29
O2F H11 H4 H 0 1 N N N N N N 18.089 3.554 22.999 5.924 -3.041 -0.086 H11 O2F 30
O2F H9 H5 H 0 1 N N N N N N 16.643 4.437 22.401 4.544 -2.275 -0.908 H9 O2F 31
O2F H10 H6 H 0 1 N N N N N N 16.780 2.664 22.149 6.035 -2.628 -1.814 H10 O2F 32
O2F H H7 H 0 1 N N N N N N 21.050 4.378 19.639 4.080 -1.614 1.081 H O2F 33
O2F H13 H8 H 0 1 N N N N N N 19.576 6.187 17.101 1.937 1.584 1.548 H13 O2F 34
O2F H14 H9 H 0 1 N N N N N N 17.883 5.930 17.643 1.628 0.145 2.561 H14 O2F 35
O2F H16 H10 H 0 1 N N N N N N 21.117 6.618 19.962 3.207 0.495 -0.969 H16 O2F 36
O2F H15 H11 H 0 1 N N N N N N 19.756 6.427 21.118 2.975 -1.284 -1.029 H15 O2F 37
O2F H2 H12 H 0 1 N N N N N N 19.304 8.486 21.244 -0.629 1.149 1.605 H2 O2F 38
O2F H18 H13 H 0 1 N N N N N N 15.018 8.404 21.248 -3.698 -2.296 0.536 H18 O2F 39
O2F H5 H14 H 0 1 N N N N N N 18.149 8.989 23.225 -1.258 -1.122 1.719 H5 O2F 40
O2F H25 H15 H 0 1 N N N N N N 16.408 7.351 23.843 -0.245 -1.741 -0.469 H25 O2F 41
O2F H24 H16 H 0 1 N N N N N N 16.273 6.859 22.120 -1.870 -2.454 -0.327 H24 O2F 42
O2F H26 H17 H 0 1 N N N N N N 17.808 6.591 23.013 -1.620 -1.000 -1.323 H26 O2F 43
O2F H3 H18 H 0 1 N N N N N N 16.249 10.299 23.281 -3.402 -0.169 1.921 H3 O2F 44
O2F H19 H19 H 0 1 N N N N N N 14.289 11.441 21.283 -3.846 -0.334 -1.870 H19 O2F 45
O2F H4 H20 H 0 1 N N N N N N 13.717 10.360 23.202 -5.668 -0.020 0.031 H4 O2F 46
O2F H20 H21 H 0 1 N N N N N N 11.916 8.687 23.289 -6.032 -3.051 0.064 H20 O2F 47
O2F H22 H22 H 0 1 N N N N N N 12.202 9.274 21.616 -7.332 -1.851 -0.135 H22 O2F 48
O2F H21 H23 H 0 1 N N N N N N 12.814 7.662 22.119 -6.074 -2.016 -1.384 H21 O2F 49
O2F H1 H24 H 0 1 N N N N N N 19.617 7.874 18.697 1.303 -1.239 0.707 H1 O2F 50
O2F H12 H26 H 0 1 N N N N N N 18.483 4.038 18.623 4.095 1.192 1.805 H12 O2F 51
O2F H17 H30 H 0 1 N N N N N N 19.958 10.929 18.469 -2.740 4.500 -1.405 H17 O2F 52
O2F H23 H31 H 0 1 N N N N N N 13.822 8.571 24.706 -5.495 -1.924 2.216 H23 O2F 53
#
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
O2F C4 N1 SING N N 1
O2F C4 C6 SING N N 2
O2F N1 C3 SING N N 3
O2F O2 C9 DOUB N N 4
O2F C6 S SING N N 5
O2F C6 C5 SING N N 6
O2F O1 C9 SING N N 7
O2F C9 C8 SING N N 8
O2F O3 C12 DOUB N N 9
O2F C1 N SING N N 10
O2F C3 C5 SING N N 11
O2F C3 C SING N N 12
O2F S C7 SING N N 13
O2F C8 C7 SING N N 14
O2F C8 N2 DOUB N N 15
O2F C N SING N N 16
O2F C O DOUB N N 17
O2F C12 C11 SING N N 18
O2F N C2 SING N N 19
O2F C7 C15 SING N N 20
O2F N2 C10 SING N N 21
O2F C11 C10 SING N N 22
O2F C11 C13 SING N N 23
O2F C10 C15 SING N N 24
O2F C14 C13 SING N N 25
O2F C15 C16 SING N N 26
O2F C13 O4 SING N N 27
O2F C1 H7 SING N N 28
O2F C1 H8 SING N N 29
O2F C1 H6 SING N N 30
O2F C2 H11 SING N N 31
O2F C2 H9 SING N N 32
O2F C2 H10 SING N N 33
O2F C3 H SING N N 34
O2F C4 H13 SING N N 35
O2F C4 H14 SING N N 36
O2F C5 H16 SING N N 37
O2F C5 H15 SING N N 38
O2F C7 H2 SING N N 39
O2F C11 H18 SING N N 40
O2F C15 H5 SING N N 41
O2F C16 H25 SING N N 42
O2F C16 H24 SING N N 43
O2F C16 H26 SING N N 44
O2F C10 H3 SING N N 45
O2F C12 H19 SING N N 46
O2F C13 H4 SING N N 47
O2F C14 H20 SING N N 48
O2F C14 H22 SING N N 49
O2F C14 H21 SING N N 50
O2F C6 H1 SING N N 51
O2F N1 H12 SING N N 52
O2F O1 H17 SING N N 53
O2F O4 H23 SING N N 54
#
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
O2F InChI InChI 1.06 "InChI=1S/C17H27N3O5S/c1-8-13(11(7-21)9(2)22)19-14(17(24)25)15(8)26-10-5-12(18-6-10)16(23)20(3)4/h7-13,15,18,22H,5-6H2,1-4H3,(H,24,25)/t8-,9-,10+,11-,12+,13-,15-/m1/s1"
O2F InChIKey InChI 1.06 UUIYVKJXUXGPKB-UUDPXGIYSA-N
O2F 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)N(C)C)[C@@H]1C)C(O)=O"
O2F SMILES CACTVS 3.385 "C[CH](O)[CH](C=O)[CH]1N=C([CH](S[CH]2CN[CH](C2)C(=O)N(C)C)[CH]1C)C(O)=O"
O2F 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)N(C)C"
O2F SMILES "OpenEye OEToolkits" 3.1.0.0 "CC1C(C(=NC1C(C=O)C(C)O)C(=O)O)SC2CC(NC2)C(=O)N(C)C"
#
_pdbx_chem_comp_identifier.comp_id O2F
_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~{S})-5-(dimethylcarbamoyl)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"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
O2F "Create component" 2022-08-26 PDBE
O2F "Initial release" 2023-03-08 RCSB
O2F "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id O2F
_pdbx_chem_comp_synonyms.name "Meropenem, bound form"
_pdbx_chem_comp_synonyms.provenance AUTHOR
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id O2F
_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 ?
#