data_8YF
#
_chem_comp.id 8YF
_chem_comp.name
;(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole
-5-carboxylic acid
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H19 N3 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Imipenem, hydrolyzed form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-11-08
_chem_comp.pdbx_modified_date 2020-06-17
_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 317.361
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8YF
_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 5YPI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
# #
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.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
8YF C62 C1 C 0 1 N N N -40.041 -13.842 4.325 -4.337 -1.656 2.025 C62 8YF 1
8YF C61 C2 C 0 1 N N R -41.119 -14.925 4.232 -4.266 -1.015 0.637 C61 8YF 2
8YF O62 O1 O 0 1 N N N -42.379 -14.375 4.624 -4.312 0.407 0.767 O62 8YF 3
8YF C6 C3 C 0 1 N N S -41.225 -15.443 2.796 -2.959 -1.423 -0.046 C6 8YF 4
8YF C7 C4 C 0 1 N N N -42.254 -16.576 2.735 -2.889 -0.791 -1.413 C7 8YF 5
8YF O71 O2 O 0 1 N N N -41.857 -17.679 2.300 -3.791 -0.087 -1.800 O71 8YF 6
8YF O72 O3 O 0 1 N N N -43.426 -16.304 3.093 -1.823 -1.010 -2.200 O72 8YF 7
8YF C5 C5 C 0 1 N N R -41.736 -14.337 1.876 -1.773 -0.948 0.796 C5 8YF 8
8YF C1 C6 C 0 1 N N N -40.714 -13.815 1.089 -0.446 -1.312 0.107 C1 8YF 9
8YF N4 N1 N 0 1 N N N -42.627 -14.977 0.893 -1.760 0.518 0.883 N4 8YF 10
8YF C3 C7 C 0 1 N N N -41.884 -15.157 -0.188 -0.571 1.004 0.316 C3 8YF 11
8YF C31 C8 C 0 1 N N N -42.289 -15.919 -1.206 -0.244 2.378 0.237 C31 8YF 12
8YF O31 O4 O 0 1 N N N -41.473 -16.431 -2.008 0.847 2.721 -0.181 O31 8YF 13
8YF O32 O5 O 0 1 N N N -43.508 -16.172 -1.325 -1.141 3.309 0.626 O32 8YF 14
8YF C2 C9 C 0 1 N N N -40.754 -14.460 -0.079 0.227 0.018 -0.147 C2 8YF 15
8YF S21 S1 S 0 1 N N N -39.518 -14.339 -1.303 1.793 0.244 -0.921 S21 8YF 16
8YF C22 C10 C 0 1 N N N -40.388 -13.240 -2.478 2.866 -0.545 0.305 C22 8YF 17
8YF C23 C11 C 0 1 N N N -40.197 -13.675 -3.932 4.329 -0.359 -0.102 C23 8YF 18
8YF N24 N2 N 0 1 N N N -38.838 -14.211 -4.084 5.197 -0.998 0.890 N24 8YF 19
8YF C25 C12 C 0 1 N N N -38.321 -14.526 -5.279 6.558 -0.961 0.735 C25 8YF 20
8YF N26 N3 N 0 1 N N N -37.083 -15.011 -5.358 7.076 -0.361 -0.286 N26 8YF 21
8YF H1 H1 H 0 1 N N N -39.975 -13.478 5.361 -4.301 -2.741 1.926 H1 8YF 22
8YF H2 H2 H 0 1 N N N -39.071 -14.263 4.021 -3.492 -1.319 2.625 H2 8YF 23
8YF H3 H3 H 0 1 N N N -40.302 -13.006 3.659 -5.268 -1.366 2.512 H3 8YF 24
8YF H4 H4 H 0 1 N N N -40.844 -15.760 4.893 -5.110 -1.353 0.037 H4 8YF 25
8YF H5 H5 H 0 1 N N N -42.320 -14.051 5.515 -5.115 0.737 1.193 H5 8YF 26
8YF H6 H6 H 0 1 N N N -40.245 -15.803 2.450 -2.923 -2.507 -0.145 H6 8YF 27
8YF H7 H7 H 0 1 N N N -43.977 -17.070 2.984 -1.824 -0.584 -3.067 H7 8YF 28
8YF H8 H8 H 0 1 N N N -42.264 -13.565 2.454 -1.816 -1.387 1.793 H8 8YF 29
8YF H9 H9 H 0 1 N N N -39.741 -13.976 1.577 0.168 -1.928 0.764 H9 8YF 30
8YF H10 H10 H 0 1 N N N -40.871 -12.738 0.931 -0.635 -1.831 -0.833 H10 8YF 31
8YF H11 H11 H 0 1 N N N -43.406 -14.384 0.688 -2.462 1.064 1.270 H11 8YF 32
8YF H12 H12 H 0 1 N N N -43.640 -16.758 -2.061 -0.827 4.220 0.536 H12 8YF 33
8YF H13 H13 H 0 1 N N N -39.999 -12.218 -2.361 2.699 -0.090 1.281 H13 8YF 34
8YF H14 H14 H 0 1 N N N -41.463 -13.252 -2.244 2.636 -1.610 0.357 H14 8YF 35
8YF H15 H15 H 0 1 N N N -40.331 -12.810 -4.599 4.496 -0.815 -1.078 H15 8YF 36
8YF H16 H16 H 0 1 N N N -40.933 -14.452 -4.186 4.559 0.705 -0.154 H16 8YF 37
8YF H17 H17 H 0 1 N N N -38.906 -14.387 -6.176 7.198 -1.432 1.467 H17 8YF 38
8YF H18 H18 H 0 1 N N N -36.816 -15.205 -6.302 8.039 -0.334 -0.396 H18 8YF 39
8YF H20 H20 H 0 1 N N N -38.279 -14.346 -3.266 4.808 -1.448 1.657 H20 8YF 40
# #
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
8YF N26 C25 DOUB N N 1
8YF C25 N24 SING N N 2
8YF N24 C23 SING N N 3
8YF C23 C22 SING N N 4
8YF C22 S21 SING N N 5
8YF O31 C31 DOUB N N 6
8YF O32 C31 SING N N 7
8YF S21 C2 SING N N 8
8YF C31 C3 SING N N 9
8YF C3 C2 DOUB N N 10
8YF C3 N4 SING N N 11
8YF C2 C1 SING N N 12
8YF N4 C5 SING N N 13
8YF C1 C5 SING N N 14
8YF C5 C6 SING N N 15
8YF O71 C7 DOUB N N 16
8YF C7 C6 SING N N 17
8YF C7 O72 SING N N 18
8YF C6 C61 SING N N 19
8YF C61 C62 SING N N 20
8YF C61 O62 SING N N 21
8YF C62 H1 SING N N 22
8YF C62 H2 SING N N 23
8YF C62 H3 SING N N 24
8YF C61 H4 SING N N 25
8YF O62 H5 SING N N 26
8YF C6 H6 SING N N 27
8YF O72 H7 SING N N 28
8YF C5 H8 SING N N 29
8YF C1 H9 SING N N 30
8YF C1 H10 SING N N 31
8YF N4 H11 SING N N 32
8YF O32 H12 SING N N 33
8YF C22 H13 SING N N 34
8YF C22 H14 SING N N 35
8YF C23 H15 SING N N 36
8YF C23 H16 SING N N 37
8YF C25 H17 SING N N 38
8YF N26 H18 SING N N 39
8YF N24 H20 SING N N 40
# #
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
8YF InChI InChI 1.03 "InChI=1S/C12H19N3O5S/c1-6(16)9(11(17)18)7-4-8(10(15-7)12(19)20)21-3-2-14-5-13/h5-7,9,15-16H,2-4H2,1H3,(H2,13,14)(H,17,18)(H,19,20)/t6-,7-,9-/m1/s1"
8YF InChIKey InChI 1.03 KSLAOLVLEKIZMQ-ZXFLCMHBSA-N
8YF SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O)[C@H]([C@H]1CC(=C(N1)C(O)=O)SCCNC=N)C(O)=O"
8YF SMILES CACTVS 3.385 "C[CH](O)[CH]([CH]1CC(=C(N1)C(O)=O)SCCNC=N)C(O)=O"
8YF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C/NCCSC1=C(N[C@H](C1)[C@@H]([C@@H](C)O)C(=O)O)C(=O)O"
8YF SMILES "OpenEye OEToolkits" 2.0.6 "CC(C(C1CC(=C(N1)C(=O)O)SCCNC=N)C(=O)O)O"
#
_pdbx_chem_comp_identifier.comp_id 8YF
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "(2~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1~{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
8YF "Create component" 2017-11-08 PDBJ
8YF "Initial release" 2018-02-21 RCSB
8YF "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 8YF
_pdbx_chem_comp_synonyms.name "Imipenem, hydrolyzed form"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##