data_VEE # _chem_comp.id VEE _chem_comp.name "(1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H30 N4 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N-alkyl mannocyclophellitol aziridine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-11 _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 330.423 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VEE _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 7ODJ _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 VEE C1 C1 C 0 1 N N N N N N 28.659 13.376 5.756 4.619 -1.418 1.316 C1 VEE 1 VEE C2 C2 C 0 1 N N R N N N 27.541 14.105 6.526 5.063 -1.640 -0.131 C2 VEE 2 VEE C3 C3 C 0 1 N N R N N N 27.065 13.308 7.731 5.610 -0.330 -0.703 C3 VEE 3 VEE C4 C4 C 0 1 N N R N N N 28.194 13.095 8.759 4.517 0.739 -0.664 C4 VEE 4 VEE C5 C5 C 0 1 N N R N N N 29.575 13.231 8.132 4.072 0.961 0.783 C5 VEE 5 VEE C6 C6 C 0 1 N N S N N N 29.591 12.584 6.682 3.525 -0.348 1.355 C6 VEE 6 VEE C8 C7 C 0 1 N N N N N N 30.717 12.836 9.060 2.979 2.031 0.822 C8 VEE 7 VEE C14 C8 C 0 1 N N N N N N 30.510 10.280 6.569 1.111 -0.395 1.182 C14 VEE 8 VEE C15 C9 C 0 1 N N N N N N 30.215 8.849 6.244 -0.053 -0.751 0.255 C15 VEE 9 VEE C16 C10 C 0 1 N N N N N N 31.441 7.922 6.392 -1.372 -0.339 0.910 C16 VEE 10 VEE C17 C11 C 0 1 N N N N N N 31.173 6.468 6.039 -2.536 -0.695 -0.018 C17 VEE 11 VEE C18 C12 C 0 1 N N N N N N 31.804 5.454 6.892 -3.855 -0.282 0.638 C18 VEE 12 VEE C19 C13 C 0 1 N N N N N N 31.341 4.035 6.616 -5.019 -0.638 -0.290 C19 VEE 13 VEE C20 C14 C 0 1 N N N N N N 30.425 3.398 7.658 -6.338 -0.225 0.365 C20 VEE 14 VEE C21 C15 C 0 1 N N N N N N 30.869 1.995 8.084 -7.502 -0.581 -0.562 C21 VEE 15 VEE N7 N1 N 0 1 N N N N N N 29.280 11.119 6.630 2.377 -0.792 0.553 N7 VEE 16 VEE O9 O1 O 0 1 N N N N N N 30.641 11.518 9.508 3.527 3.288 0.421 O9 VEE 17 VEE O11 O2 O 0 1 N N N N N N 28.071 14.105 9.750 5.028 1.962 -1.198 O11 VEE 18 VEE O12 O3 O 0 1 N N N N N N 26.562 12.087 7.231 6.026 -0.538 -2.054 O12 VEE 19 VEE O13 O4 O 0 1 N N N N N N 26.409 14.328 5.679 3.947 -2.071 -0.911 O13 VEE 20 VEE H1 H1 H 0 1 N N N N N N 28.198 12.680 5.040 4.229 -2.351 1.724 H1 VEE 21 VEE H2 H2 H 0 1 N N N N N N 27.937 15.069 6.879 5.842 -2.402 -0.159 H2 VEE 22 VEE H3 H3 H 0 1 N N N N N N 26.258 13.871 8.222 6.462 -0.001 -0.107 H3 VEE 23 VEE H4 H4 H 0 1 N N N N N N 28.092 12.095 9.205 3.665 0.410 -1.259 H4 VEE 24 VEE H5 H5 H 0 1 N N N N N N 29.707 14.309 7.955 4.924 1.290 1.379 H5 VEE 25 VEE H6 H6 H 0 1 N N N N N N 30.613 12.716 6.296 3.208 -0.190 2.386 H6 VEE 26 VEE H24 H7 H 0 1 N N N N N N 31.666 12.965 8.519 2.174 1.752 0.143 H24 VEE 27 VEE H29 H8 H 0 1 N N N N N N 30.701 13.502 9.935 2.586 2.112 1.836 H29 VEE 28 VEE H7 H9 H 0 1 N N N N N N 31.014 10.323 7.546 1.115 0.679 1.363 H7 VEE 29 VEE H8 H10 H 0 1 N N N N N N 31.176 10.687 5.794 0.995 -0.923 2.129 H8 VEE 30 VEE H10 H11 H 0 1 N N N N N N 29.859 8.794 5.205 0.063 -0.224 -0.692 H10 VEE 31 VEE H9 H12 H 0 1 N N N N N N 29.425 8.493 6.922 -0.058 -1.826 0.074 H9 VEE 32 VEE H11 H13 H 0 1 N N N N N N 31.781 7.966 7.437 -1.488 -0.866 1.857 H11 VEE 33 VEE H12 H14 H 0 1 N N N N N N 32.237 8.296 5.731 -1.368 0.736 1.091 H12 VEE 34 VEE H13 H15 H 0 1 N N N N N N 30.085 6.310 6.083 -2.420 -0.167 -0.965 H13 VEE 35 VEE H14 H16 H 0 1 N N N N N N 31.526 6.304 5.010 -2.541 -1.769 -0.199 H14 VEE 36 VEE H16 H17 H 0 1 N N N N N N 32.892 5.499 6.735 -3.971 -0.809 1.585 H16 VEE 37 VEE H15 H18 H 0 1 N N N N N N 31.575 5.694 7.941 -3.851 0.793 0.819 H15 VEE 38 VEE H18 H19 H 0 1 N N N N N N 30.802 4.041 5.657 -4.903 -0.111 -1.237 H18 VEE 39 VEE H17 H20 H 0 1 N N N N N N 32.237 3.403 6.529 -5.023 -1.713 -0.471 H17 VEE 40 VEE H20 H21 H 0 1 N N N N N N 30.408 4.044 8.548 -6.454 -0.752 1.312 H20 VEE 41 VEE H19 H22 H 0 1 N N N N N N 29.412 3.330 7.236 -6.334 0.850 0.546 H19 VEE 42 VEE H23 H26 H 0 1 N N N N N N 28.726 10.937 5.818 2.408 -1.788 0.398 H23 VEE 43 VEE H25 H28 H 0 1 N N N N N N 31.377 11.334 10.079 2.889 4.014 0.423 H25 VEE 44 VEE H26 H29 H 0 1 N N N N N N 28.757 13.998 10.399 5.329 1.896 -2.114 H26 VEE 45 VEE H27 H30 H 0 1 N N N N N N 26.251 11.553 7.953 6.719 -1.204 -2.155 H27 VEE 46 VEE H28 H31 H 0 1 N N N N N N 25.730 14.778 6.169 4.156 -2.231 -1.842 H28 VEE 47 VEE N1 N2 N 0 1 N Y N N N N ? ? ? -8.765 -0.186 0.065 N1 VEE 48 VEE N2 N3 N 1 1 N N N N N N ? ? ? -9.437 0.558 -0.443 N2 VEE 49 VEE N3 N4 N -1 1 N N N N N N ? ? ? -10.109 1.302 -0.952 N3 VEE 50 VEE H21 H33 H 0 1 N N N N N N 31.599 1.475 7.446 -7.386 -0.054 -1.509 H21 VEE 51 VEE H22 H34 H 0 1 N N N N N N 31.131 1.841 9.141 -7.506 -1.656 -0.743 H22 VEE 52 VEE H31 H32 H 0 1 N N N N N N 29.255 14.122 5.210 5.470 -1.089 1.912 H31 VEE 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 VEE O13 C2 SING N N 1 VEE C1 C2 SING N N 2 VEE C1 C6 SING N N 3 VEE C17 C16 SING N N 4 VEE C17 C18 SING N N 5 VEE C15 C16 SING N N 6 VEE C15 C14 SING N N 7 VEE C2 C3 SING N N 8 VEE C14 N7 SING N N 9 VEE C19 C18 SING N N 10 VEE C19 C20 SING N N 11 VEE N7 C6 SING N N 12 VEE C6 C5 SING N N 13 VEE O12 C3 SING N N 14 VEE C20 C21 SING N N 15 VEE C3 C4 SING N N 16 VEE C5 C4 SING N N 17 VEE C5 C8 SING N N 18 VEE C4 O11 SING N N 19 VEE C8 O9 SING N N 20 VEE C1 H1 SING N N 21 VEE C2 H2 SING N N 22 VEE C3 H3 SING N N 23 VEE C4 H4 SING N N 24 VEE C5 H5 SING N N 25 VEE C6 H6 SING N N 26 VEE C8 H24 SING N N 27 VEE C8 H29 SING N N 28 VEE C14 H7 SING N N 29 VEE C14 H8 SING N N 30 VEE C15 H10 SING N N 31 VEE C15 H9 SING N N 32 VEE C16 H11 SING N N 33 VEE C16 H12 SING N N 34 VEE C17 H13 SING N N 35 VEE C17 H14 SING N N 36 VEE C18 H16 SING N N 37 VEE C18 H15 SING N N 38 VEE C19 H18 SING N N 39 VEE C19 H17 SING N N 40 VEE C20 H20 SING N N 41 VEE C20 H19 SING N N 42 VEE N7 H23 SING N N 43 VEE O9 H25 SING N N 44 VEE O11 H26 SING N N 45 VEE O12 H27 SING N N 46 VEE O13 H28 SING N N 47 VEE C21 N1 SING N N 48 VEE N1 N2 DOUB N N 49 VEE N2 N3 DOUB N N 50 VEE C21 H21 SING N N 51 VEE C21 H22 SING N N 52 VEE C1 H31 SING N N 53 # 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 VEE InChI InChI 1.03 "InChI=1S/C15H30N4O4/c16-19-18-8-6-4-2-1-3-5-7-17-12-9-13(21)15(23)14(22)11(12)10-20/h11-15,17,20-23H,1-10H2/t11-,12-,13+,14+,15+/m0/s1" VEE InChIKey InChI 1.03 GOBIPKNKUJPACR-VQJWOFKYSA-N VEE SMILES_CANONICAL CACTVS 3.385 "OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)C[C@@H]1NCCCCCCCCN=[N+]=[N-]" VEE SMILES CACTVS 3.385 "OC[CH]1[CH](O)[CH](O)[CH](O)C[CH]1NCCCCCCCCN=[N+]=[N-]" VEE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@@H]([C@H]([C@@H]([C@@H]1O)O)O)CO)NCCCCCCCCN=[N+]=[N-]" VEE SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(C1O)O)O)CO)NCCCCCCCCN=[N+]=[N-]" # _pdbx_chem_comp_identifier.comp_id VEE _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(1~{R},2~{R},3~{R},4~{R},5~{S})-5-(8-azidooctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VEE _pdbx_chem_comp_synonyms.name "N-alkyl mannocyclophellitol aziridine" _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 VEE "Create component" 2021-05-11 PDBE VEE "Other modification" 2021-07-21 PDBE VEE "Initial release" 2022-02-02 RCSB VEE "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id VEE _pdbx_chem_comp_pcm.modified_residue_id GLU _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 C1 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #