data_CED
#
_chem_comp.id CED
_chem_comp.name "5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H16 N2 O4 S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "DEGRADED CEPHALORIDINE, open form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-12-20
_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 340.418
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CED
_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 1GHM
_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
CED S1 S1 S 0 1 N N N N N N 2.579 -6.720 -10.994 -1.925 -1.799 0.244 S1 CED 1
CED C2 C2 C 0 1 N N N N N N 4.286 -6.291 -10.587 -3.516 -2.083 -0.590 C2 CED 2
CED C3 C3 C 0 1 N N N N N N 5.326 -6.340 -11.665 -4.360 -0.846 -0.488 C3 CED 3
CED "C3'" "C3'" C 0 1 N N N N N N 6.498 -5.548 -11.511 -5.848 -1.011 -0.661 "C3'" CED 4
CED C4 C4 C 0 1 N N N N N N 5.113 -7.252 -12.872 -3.915 0.368 -0.261 C4 CED 5
CED "C4'" "C4'" C 0 1 N N N N N N 6.155 -7.370 -13.992 -4.926 1.440 -0.220 "C4'" CED 6
CED O4A O4A O 0 1 N N N N N N 7.240 -6.745 -13.974 -6.084 1.194 -0.496 O4A CED 7
CED O4B O4B O 0 1 N N N N N N 5.795 -8.134 -14.883 -4.567 2.693 0.124 O4B CED 8
CED N5 N5 N 0 1 N N N N N N 3.982 -8.021 -13.039 -2.597 0.755 -0.054 N5 CED 9
CED C6 C6 C 0 1 N N R N N N 2.848 -8.123 -12.130 -1.484 -0.147 -0.386 C6 CED 10
CED C7 C7 C 0 1 N N R N N N 2.939 -9.479 -11.350 -0.199 0.341 0.287 C7 CED 11
CED C8 C8 C 0 1 N N N N N N 3.640 -10.513 -12.248 -0.410 0.417 1.777 C8 CED 12
CED O9 O9 O 0 1 N N N N N N 4.829 -10.838 -12.046 0.279 -0.241 2.519 O9 CED 13
CED N10 N10 N 0 1 N N N N N N 3.781 -9.448 -10.092 0.890 -0.594 -0.005 N10 CED 14
CED C11 C11 C 0 1 N N N N N N 3.156 -9.388 -8.792 2.169 -0.168 0.024 C11 CED 15
CED O12 O12 O 0 1 N N N N N N 1.921 -9.347 -8.634 2.417 0.988 0.292 O12 CED 16
CED C13 C13 C 0 1 N N N N N N 4.111 -9.409 -7.598 3.290 -1.130 -0.276 C13 CED 17
CED C14 C14 C 0 1 Y N N N N N 4.654 -8.038 -7.345 4.610 -0.409 -0.177 C14 CED 18
CED C15 C15 C 0 1 Y N N N N N 3.900 -6.805 -7.052 5.345 -0.299 0.930 C15 CED 19
CED C16 C16 C 0 1 Y N N N N N 4.865 -5.771 -6.971 6.524 0.410 0.779 C16 CED 20
CED C17 C17 C 0 1 Y N N N N N 6.174 -6.109 -7.129 6.746 0.876 -0.450 C17 CED 21
CED S19 S19 S 0 1 Y N N N N N 6.295 -7.785 -7.414 5.420 0.409 -1.507 S19 CED 22
CED H21 H21 H 0 1 N N N N N N 4.267 -5.254 -10.221 -3.340 -2.318 -1.640 H21 CED 23
CED H22 H22 H 0 1 N N N N N N 4.608 -7.002 -9.812 -4.033 -2.916 -0.113 H22 CED 24
CED "H3'1" "H3'1" H 0 0 N N N N N N 7.157 -5.694 -12.380 -6.078 -2.061 -0.842 "H3'1" CED 25
CED "H3'2" "H3'2" H 0 0 N N N N N N 6.217 -4.487 -11.439 -6.358 -0.678 0.242 "H3'2" CED 26
CED "H3'3" "H3'3" H 0 0 N N N N N N 7.027 -5.850 -10.595 -6.183 -0.415 -1.510 "H3'3" CED 27
CED HO4 HO4 H 0 1 N N N N N N 6.466 -8.177 -15.554 -5.265 3.362 0.136 HO4 CED 28
CED HN5 HN5 H 0 1 N N N N N N 3.581 -7.679 -13.889 -2.408 1.632 0.314 HN5 CED 29
CED H6 H6 H 0 1 N N N N N N 1.956 -8.088 -12.773 -1.347 -0.186 -1.466 H6 CED 30
CED H7 H7 H 0 1 N N N N N N 1.899 -9.712 -11.077 0.058 1.329 -0.095 H7 CED 31
CED H8 H8 H 0 1 N N N N N N 3.096 -10.964 -13.065 -1.178 1.061 2.181 H8 CED 32
CED HN1 HN1 H 0 1 N N N N N N 4.778 -9.469 -10.162 0.692 -1.518 -0.219 HN1 CED 33
CED H131 H131 H 0 0 N N N N N N 3.568 -9.753 -6.706 3.268 -1.949 0.443 H131 CED 34
CED H132 H132 H 0 0 N N N N N N 4.944 -10.094 -7.813 3.167 -1.527 -1.284 H132 CED 35
CED H15 H15 H 0 1 N N N N N N 2.832 -6.710 -6.925 5.043 -0.731 1.873 H15 CED 36
CED H16 H16 H 0 1 N N N N N N 4.572 -4.748 -6.790 7.212 0.574 1.596 H16 CED 37
CED H17 H17 H 0 1 N N N N N N 7.006 -5.422 -7.081 7.610 1.450 -0.752 H17 CED 38
#
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
CED S1 C2 SING N N 1
CED S1 C6 SING N N 2
CED C2 C3 SING N N 3
CED C2 H21 SING N N 4
CED C2 H22 SING N N 5
CED C3 "C3'" SING N N 6
CED C3 C4 DOUB N N 7
CED "C3'" "H3'1" SING N N 8
CED "C3'" "H3'2" SING N N 9
CED "C3'" "H3'3" SING N N 10
CED C4 "C4'" SING N N 11
CED C4 N5 SING N N 12
CED "C4'" O4A DOUB N N 13
CED "C4'" O4B SING N N 14
CED O4B HO4 SING N N 15
CED N5 C6 SING N N 16
CED N5 HN5 SING N N 17
CED C6 C7 SING N N 18
CED C6 H6 SING N N 19
CED C7 C8 SING N N 20
CED C7 N10 SING N N 21
CED C7 H7 SING N N 22
CED C8 O9 DOUB N N 23
CED C8 H8 SING N N 24
CED N10 C11 SING N N 25
CED N10 HN1 SING N N 26
CED C11 O12 DOUB N N 27
CED C11 C13 SING N N 28
CED C13 C14 SING N N 29
CED C13 H131 SING N N 30
CED C13 H132 SING N N 31
CED C14 C15 DOUB Y N 32
CED C14 S19 SING Y N 33
CED C15 C16 SING Y N 34
CED C15 H15 SING N N 35
CED C16 C17 DOUB Y N 36
CED C16 H16 SING N N 37
CED C17 S19 SING Y N 38
CED C17 H17 SING N N 39
#
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
CED SMILES ACDLabs 12.01 "O=CC(NC(=O)Cc1sccc1)C2SCC(=C(C(=O)O)N2)C"
CED InChI InChI 1.03 "InChI=1S/C14H16N2O4S2/c1-8-7-22-13(16-12(8)14(19)20)10(6-17)15-11(18)5-9-3-2-4-21-9/h2-4,6,10,13,16H,5,7H2,1H3,(H,15,18)(H,19,20)/t10-,13-/m1/s1"
CED InChIKey InChI 1.03 SFVACKBZMIZHCK-ZWNOBZJWSA-N
CED SMILES_CANONICAL CACTVS 3.370 "CC1=C(N[C@H](SC1)[C@H](NC(=O)Cc2sccc2)C=O)C(O)=O"
CED SMILES CACTVS 3.370 "CC1=C(N[CH](SC1)[CH](NC(=O)Cc2sccc2)C=O)C(O)=O"
CED SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=C(N[C@H](SC1)[C@@H](C=O)NC(=O)Cc2cccs2)C(=O)O"
CED SMILES "OpenEye OEToolkits" 1.7.2 "CC1=C(NC(SC1)C(C=O)NC(=O)Cc2cccs2)C(=O)O"
#
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
CED "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-5-methyl-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid"
CED "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(2R)-5-methyl-2-[(1R)-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-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
CED "Create component" 2000-12-20 RCSB
CED "Modify descriptor" 2011-06-04 RCSB
CED "Modify synonyms" 2011-07-31 PDBJ
CED "Modify synonyms" 2020-06-05 PDBE
CED "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CED
_pdbx_chem_comp_synonyms.name "DEGRADED CEPHALORIDINE, open form"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CED
_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 C8
_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 ?
#