data_CD7 # _chem_comp.id CD7 _chem_comp.name "(2S,5Z)-1-formyl-5-imino-N'-[(3R)-1-(sulfooxy)pyrrolidine-3-carbonyl]piperidine-2-carbohydrazide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H19 N5 O7 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "open form - WCK 5153" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-20 _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 377.374 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CD7 _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 6B1Y _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 CD7 OAB O1 O 0 1 N N N N N N 8.877 1.128 -2.180 -4.309 -3.095 -0.569 OAB CD7 1 CD7 CAE C1 C 0 1 N N N N N N 9.148 0.075 -2.771 -3.841 -1.991 -0.387 CAE CD7 2 CD7 N N1 N 0 1 N N N N N N 10.406 -0.334 -3.016 -4.620 -0.899 -0.517 N CD7 3 CD7 CAL C2 C 0 1 N N N N N N 10.650 -1.685 -3.577 -6.010 -1.019 -0.987 CAL CD7 4 CD7 CAP C3 C 0 1 N N N N N N 11.614 -2.230 -2.640 -6.886 -0.232 -0.035 CAP CD7 5 CD7 NAA N2 N 0 1 N N N N N N 11.649 -3.526 -2.404 -7.976 -0.725 0.419 NAA CD7 6 CD7 CAH C4 C 0 1 N N N N N N 12.549 -1.498 -1.876 -6.433 1.156 0.363 CAH CD7 7 CD7 CB C5 C 0 1 N N N N N N 12.152 -0.118 -1.575 -4.994 1.072 0.884 CB CD7 8 CD7 CA C6 C 0 1 N N S N N N 11.509 0.587 -2.783 -4.103 0.435 -0.186 CA CD7 9 CD7 C C7 C 0 1 N N N N N N 12.365 0.850 -3.913 -2.698 0.312 0.345 C CD7 10 CD7 O O2 O 0 1 N N N N N N 11.966 0.656 -5.076 -2.442 -0.511 1.199 O CD7 11 CD7 NAO N3 N 0 1 N N N N N N 13.600 1.368 -3.615 -1.726 1.117 -0.128 NAO CD7 12 CD7 NAN N4 N 0 1 N N N N N N 14.310 1.905 -4.604 -0.420 1.003 0.366 NAN CD7 13 CD7 CAQ C8 C 0 1 N N N N N N 14.031 3.167 -4.988 0.552 1.808 -0.107 CAQ CD7 14 CD7 OAC O3 O 0 1 N N N N N N 13.016 3.739 -4.633 0.296 2.631 -0.960 OAC CD7 15 CD7 CAS C9 C 0 1 N N R N N N 15.083 3.830 -5.911 1.957 1.686 0.424 CAS CD7 16 CD7 CAI C10 C 0 1 N N N N N N 16.318 4.157 -5.177 2.893 2.706 -0.263 CAI CD7 17 CD7 CAF C11 C 0 1 N N N N N N 15.805 5.437 -4.358 4.214 1.949 -0.493 CAF CD7 18 CD7 NAM N5 N 0 1 N N N N N N 14.712 6.061 -5.205 4.038 0.590 0.063 NAM CD7 19 CD7 CAK C12 C 0 1 N N N N N N 14.645 5.209 -6.409 2.577 0.323 0.025 CAK CD7 20 CD7 H1 H1 H 0 1 N Y N N N N 8.332 -0.548 -3.107 -2.801 -1.884 -0.116 H1 CD7 21 CD7 H2 H2 H 0 1 N N N N N N 9.727 -2.283 -3.595 -6.096 -0.608 -1.994 H2 CD7 22 CD7 H3 H3 H 0 1 N N N N N N 11.068 -1.627 -4.593 -6.311 -2.066 -0.988 H3 CD7 23 CD7 H4 H4 H 0 1 N N N N N N 12.338 -3.764 -1.719 -8.526 -0.208 1.029 H4 CD7 24 CD7 H5 H5 H 0 1 N N N N N N 12.700 -2.026 -0.923 -6.471 1.816 -0.503 H5 CD7 25 CD7 H6 H6 H 0 1 N N N N N N 13.497 -1.468 -2.433 -7.084 1.542 1.148 H6 CD7 26 CD7 H7 H7 H 0 1 N N N N N N 13.045 0.448 -1.271 -4.630 2.074 1.111 H7 CD7 27 CD7 H8 H8 H 0 1 N N N N N N 11.427 -0.132 -0.748 -4.970 0.463 1.787 H8 CD7 28 CD7 H9 H9 H 0 1 N N N N N N 11.096 1.542 -2.425 -4.101 1.057 -1.081 H9 CD7 29 CD7 H10 H10 H 0 1 N N N N N N 13.956 1.343 -2.681 -1.931 1.776 -0.810 H10 CD7 30 CD7 H11 H11 H 0 1 N N N N N N 15.035 1.383 -5.053 -0.215 0.345 1.048 H11 CD7 31 CD7 H12 H12 H 0 1 N N N N N N 15.298 3.171 -6.765 1.972 1.817 1.506 H12 CD7 32 CD7 H13 H13 H 0 1 N N N N N N 16.628 3.339 -4.510 2.470 3.026 -1.215 H13 CD7 33 CD7 H14 H14 H 0 1 N N N N N N 17.145 4.409 -5.857 3.057 3.566 0.386 H14 CD7 34 CD7 H15 H15 H 0 1 N N N N N N 16.628 6.151 -4.209 4.426 1.889 -1.561 H15 CD7 35 CD7 H16 H16 H 0 1 N N N N N N 15.404 5.130 -3.381 5.029 2.461 0.019 H16 CD7 36 CD7 O1 O4 O 0 1 N N N N N N 13.821 6.068 -4.709 4.773 -0.399 -0.726 O1 CD7 37 CD7 H19 H19 H 0 1 N N N N N N 15.328 5.579 -7.188 2.308 -0.448 0.746 H19 CD7 38 CD7 H20 H20 H 0 1 N N N N N N 13.620 5.174 -6.807 2.265 0.038 -0.980 H20 CD7 39 CD7 S1 S1 S 0 1 N N N N N N ? ? ? 5.830 -1.158 0.063 S1 CD7 40 CD7 O3 O5 O 0 1 N N N N N N ? ? ? 6.570 -1.916 -0.885 O3 CD7 41 CD7 O2 O6 O 0 1 N N N N N N ? ? ? 6.428 -0.216 0.942 O2 CD7 42 CD7 O4 O7 O 0 1 N N N N N N ? ? ? 5.101 -2.164 0.942 O4 CD7 43 CD7 H17 H17 H 0 1 N N N N N N ? ? ? 5.686 -2.704 1.490 H17 CD7 44 # 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 CD7 CAK CAS SING N N 1 CD7 CAK NAM SING N N 2 CD7 CAS CAI SING N N 3 CD7 CAS CAQ SING N N 4 CD7 NAM CAF SING N N 5 CD7 CAI CAF SING N N 6 CD7 O C DOUB N N 7 CD7 CAQ OAC DOUB N N 8 CD7 CAQ NAN SING N N 9 CD7 NAN NAO SING N N 10 CD7 C NAO SING N N 11 CD7 C CA SING N N 12 CD7 CAL N SING N N 13 CD7 CAL CAP SING N N 14 CD7 N CA SING N N 15 CD7 N CAE SING N N 16 CD7 CA CB SING N N 17 CD7 CAE OAB DOUB N N 18 CD7 CAP NAA DOUB N N 19 CD7 CAP CAH SING N N 20 CD7 CAH CB SING N N 21 CD7 CAE H1 SING N N 22 CD7 CAL H2 SING N N 23 CD7 CAL H3 SING N N 24 CD7 NAA H4 SING N N 25 CD7 CAH H5 SING N N 26 CD7 CAH H6 SING N N 27 CD7 CB H7 SING N N 28 CD7 CB H8 SING N N 29 CD7 CA H9 SING N N 30 CD7 NAO H10 SING N N 31 CD7 NAN H11 SING N N 32 CD7 CAS H12 SING N N 33 CD7 CAI H13 SING N N 34 CD7 CAI H14 SING N N 35 CD7 CAF H15 SING N N 36 CD7 CAF H16 SING N N 37 CD7 NAM O1 SING N N 38 CD7 CAK H19 SING N N 39 CD7 CAK H20 SING N N 40 CD7 O1 S1 SING N N 41 CD7 S1 O3 DOUB N N 42 CD7 S1 O2 DOUB N N 43 CD7 S1 O4 SING N N 44 CD7 O4 H17 SING N N 45 # 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 CD7 SMILES ACDLabs 12.01 "O=CN1C(CCC(/C1)=N)C(NNC(=O)C2CCN(OS(=O)(=O)O)C2)=O" CD7 InChI InChI 1.03 "InChI=1S/C12H19N5O7S/c13-9-1-2-10(16(6-9)7-18)12(20)15-14-11(19)8-3-4-17(5-8)24-25(21,22)23/h7-8,10,13H,1-6H2,(H,14,19)(H,15,20)(H,21,22,23)/b13-9-/t8-,10+/m1/s1" CD7 InChIKey InChI 1.03 APRDZKRWJZJQAT-NBGMFQDKSA-N CD7 SMILES_CANONICAL CACTVS 3.385 "O[S](=O)(=O)ON1CC[C@H](C1)C(=O)NNC(=O)[C@@H]2CCC(=N)CN2C=O" CD7 SMILES CACTVS 3.385 "O[S](=O)(=O)ON1CC[CH](C1)C(=O)NNC(=O)[CH]2CCC(=N)CN2C=O" CD7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C\1/CC[C@H](N(C1)C=O)C(=O)NNC(=O)[C@@H]2CCN(C2)OS(=O)(=O)O" CD7 SMILES "OpenEye OEToolkits" 2.0.6 "C1CC(=N)CN(C1C(=O)NNC(=O)C2CCN(C2)OS(=O)(=O)O)C=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 CD7 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,5Z)-1-formyl-5-imino-N'-[(3R)-1-(sulfooxy)pyrrolidine-3-carbonyl]piperidine-2-carbohydrazide" CD7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(3~{R})-3-[[[(2~{S})-5-azanylidene-1-methanoyl-piperidin-2-yl]carbonylamino]carbamoyl]pyrrolidin-1-yl] hydrogen sulfate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CD7 "Create component" 2017-09-20 RCSB CD7 "Initial release" 2018-08-01 RCSB CD7 "Modify synonyms" 2021-03-01 PDBE CD7 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CD7 _pdbx_chem_comp_synonyms.name "open form - WCK 5153" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id CD7 _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 CAE _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 ? #