data_SD0 # _chem_comp.id SD0 _chem_comp.name "(S)-5-amino-2-(4-(2-amino-2-carboxyethyl)phenyl)-2-hydroxy-5-(hydroxymethyl)-1,3,2-dioxaborinan-2-uide" _chem_comp.type peptide-like _chem_comp.pdbx_type ATOMP _chem_comp.formula "C13 H20 B N2 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2~{S})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-$l^{3}-oxidanyl-1,3,2$l^{4}-dioxaborinan-2-yl]phenyl]propanal" _chem_comp.pdbx_formal_charge -1 _chem_comp.pdbx_initial_date 2023-08-30 _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 311.119 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SD0 _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 8QDH _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 SD0 N N N 0 1 N N N Y Y N -6.233 9.856 -21.320 -3.989 1.044 1.417 N SD0 1 SD0 CA CA C 0 1 N N S Y N N -7.173 10.251 -20.254 -4.358 0.642 0.053 CA SD0 2 SD0 C C C 0 1 N N N Y N Y -8.585 10.277 -20.929 -5.857 0.693 -0.097 C SD0 3 SD0 O O O 0 1 N N N Y N Y -9.578 9.814 -20.360 -6.563 0.669 0.883 O SD0 4 SD0 CB CB C 0 1 N N N N N N -6.940 11.598 -19.569 -3.867 -0.783 -0.209 CB SD0 5 SD0 CG CG C 0 1 Y N N N N N -7.982 11.775 -18.464 -2.361 -0.809 -0.180 CG SD0 6 SD0 CD1 CD1 C 0 1 Y N N N N N -9.197 12.408 -18.709 -1.643 -0.590 -1.341 CD1 SD0 7 SD0 CD2 CD2 C 0 1 Y N N N N N -7.795 11.196 -17.220 -1.696 -1.046 1.008 CD2 SD0 8 SD0 CE1 CE1 C 0 1 Y N N N N N -10.168 12.513 -17.711 -0.262 -0.614 -1.315 CE1 SD0 9 SD0 CE2 CE2 C 0 1 Y N N N N N -8.770 11.286 -16.226 -0.314 -1.070 1.035 CE2 SD0 10 SD0 CZ CZ C 0 1 Y N N N N N -9.966 11.960 -16.451 0.403 -0.856 -0.127 CZ SD0 11 SD0 B1 B1 B -1 1 N N N N N N -11.157 12.067 -15.307 1.959 -0.883 -0.097 B1 SD0 12 SD0 C1 C1 C 0 1 N N N N N N -10.979 9.761 -14.222 3.819 -0.517 1.284 C1 SD0 13 SD0 C2 C2 C 0 1 N N N N N N -12.329 9.350 -14.784 4.451 0.370 0.204 C2 SD0 14 SD0 C3 C3 C 0 1 N N N N N N -12.385 7.826 -14.980 4.122 1.837 0.483 C3 SD0 15 SD0 C4 C4 C 0 1 N N N N N N -12.480 10.060 -16.121 3.874 -0.038 -1.156 C4 SD0 16 SD0 N2 N2 N 0 1 N N N N N N -13.442 9.794 -13.880 5.908 0.182 0.200 N2 SD0 17 SD0 O1 O1 O 0 1 N N N N N N -10.858 11.204 -14.145 2.396 -0.478 1.132 O1 SD0 18 SD0 O2 O2 O 0 1 N N N N N N -12.351 11.503 -15.957 2.445 -0.047 -1.062 O2 SD0 19 SD0 O3 O3 O 0 1 N N N N N N -12.331 7.090 -13.769 4.713 2.659 -0.525 O3 SD0 20 SD0 O5 O5 O 0 1 N N N N N N -11.418 13.422 -14.917 2.395 -2.156 -0.337 O5 SD0 21 SD0 H H1 H 0 1 N N N Y Y N -5.305 9.820 -20.950 -4.245 2.004 1.593 H1 SD0 22 SD0 H2 H2 H 0 1 N Y N Y Y N -6.487 8.955 -21.671 -4.403 0.428 2.100 H2 SD0 23 SD0 HA HA H 0 1 N N N Y N N -7.184 9.469 -19.481 -3.898 1.322 -0.663 HA SD0 24 SD0 HB2 HB2 H 0 1 N N N N N N -5.931 11.621 -19.133 -4.257 -1.449 0.561 HB2 SD0 25 SD0 HB1 HB1 H 0 1 N N N N N N -7.040 12.409 -20.305 -4.218 -1.114 -1.187 HB1 SD0 26 SD0 HD1 HD1 H 0 1 N N N N N N -9.392 12.824 -19.686 -2.162 -0.400 -2.269 HD1 SD0 27 SD0 HD2 HD2 H 0 1 N N N N N N -6.877 10.665 -17.015 -2.257 -1.213 1.917 HD2 SD0 28 SD0 HE1 HE1 H 0 1 N N N N N N -11.091 13.032 -17.921 0.299 -0.443 -2.222 HE1 SD0 29 SD0 HE2 HE2 H 0 1 N N N N N N -8.593 10.825 -15.266 0.205 -1.255 1.964 HE2 SD0 30 SD0 H11 H11 H 0 1 N N N N N N -10.867 9.338 -13.213 4.171 -1.542 1.168 H11 SD0 31 SD0 H12 H12 H 0 1 N N N N N N -10.185 9.369 -14.874 4.092 -0.146 2.272 H12 SD0 32 SD0 H31 H31 H 0 1 N N N N N N -13.324 7.577 -15.495 3.041 1.975 0.476 H31 SD0 33 SD0 H32 H32 H 0 1 N N N N N N -11.532 7.526 -15.607 4.517 2.119 1.459 H32 SD0 34 SD0 H41 H41 H 0 1 N N N N N N -13.471 9.832 -16.541 4.186 0.678 -1.915 H41 SD0 35 SD0 H42 H42 H 0 1 N N N N N N -11.699 9.704 -16.809 4.229 -1.034 -1.421 H42 SD0 36 SD0 H21 H21 H 0 1 N N N N N N -13.357 9.335 -12.995 6.345 0.757 -0.505 H21 SD0 37 SD0 H23 H23 H 0 1 N N N N N N -13.390 10.784 -13.748 6.299 0.367 1.111 H23 SD0 38 SD0 HO3 HO3 H 0 1 N N N N N N -12.370 6.160 -13.961 4.545 3.604 -0.411 HO3 SD0 39 SD0 H4 H4 H 0 1 N N N N N N -12.106 13.437 -14.262 3.357 -2.249 -0.334 H4 SD0 40 SD0 OXT O4 O 0 1 N Y N Y N Y -8.658 10.821 -22.146 -6.407 0.764 -1.319 O4 SD0 41 SD0 HXT H3 H 0 1 N Y N Y N Y -9.555 10.782 -22.458 -7.372 0.794 -1.365 H3 SD0 42 # 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 SD0 N CA SING N N 1 SD0 C O DOUB N N 2 SD0 C CA SING N N 3 SD0 CA CB SING N N 4 SD0 CB CG SING N N 5 SD0 CD1 CG DOUB Y N 6 SD0 CD1 CE1 SING Y N 7 SD0 CG CD2 SING Y N 8 SD0 CE1 CZ DOUB Y N 9 SD0 CD2 CE2 DOUB Y N 10 SD0 CZ CE2 SING Y N 11 SD0 CZ B1 SING N N 12 SD0 C4 O2 SING N N 13 SD0 C4 C2 SING N N 14 SD0 O2 B1 SING N N 15 SD0 B1 O5 SING N N 16 SD0 B1 O1 SING N N 17 SD0 C3 C2 SING N N 18 SD0 C3 O3 SING N N 19 SD0 C2 C1 SING N N 20 SD0 C2 N2 SING N N 21 SD0 C1 O1 SING N N 22 SD0 N H SING N N 23 SD0 N H2 SING N N 24 SD0 CA HA SING N N 25 SD0 CB HB2 SING N N 26 SD0 CB HB1 SING N N 27 SD0 CD1 HD1 SING N N 28 SD0 CD2 HD2 SING N N 29 SD0 CE1 HE1 SING N N 30 SD0 CE2 HE2 SING N N 31 SD0 C1 H11 SING N N 32 SD0 C1 H12 SING N N 33 SD0 C3 H31 SING N N 34 SD0 C3 H32 SING N N 35 SD0 C4 H41 SING N N 36 SD0 C4 H42 SING N N 37 SD0 N2 H21 SING N N 38 SD0 N2 H23 SING N N 39 SD0 O3 HO3 SING N N 40 SD0 O5 H4 SING N N 41 SD0 C OXT SING N N 42 SD0 OXT HXT SING N N 43 # 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 SD0 InChI InChI 1.06 "InChI=1S/C13H20BN2O6/c15-11(12(18)19)5-9-1-3-10(4-2-9)14(20)21-7-13(16,6-17)8-22-14/h1-4,11,17,20H,5-8,15-16H2,(H,18,19)/q-1/t11-,13-,14+/m0/s1" SD0 InChIKey InChI 1.06 ODSWUTOGRMJOFF-FPMFFAJLSA-N SD0 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](Cc1ccc(cc1)[B-]2(O)OCC(N)(CO)CO2)C(O)=O" SD0 SMILES CACTVS 3.385 "N[CH](Cc1ccc(cc1)[B-]2(O)OCC(N)(CO)CO2)C(O)=O" SD0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[B-]1(OCC(CO1)(CO)N)(c2ccc(cc2)C[C@@H](C(=O)O)N)O" SD0 SMILES "OpenEye OEToolkits" 2.0.7 "[B-]1(OCC(CO1)(CO)N)(c2ccc(cc2)CC(C(=O)O)N)O" # _pdbx_chem_comp_identifier.comp_id SD0 _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 "(2~{S})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-oxidanyl-1,3-dioxa-2-boranuidacyclohex-2-yl]phenyl]propanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SD0 _pdbx_chem_comp_synonyms.name "(2~{S})-2-azanyl-3-[4-[5-azanyl-5-(hydroxymethyl)-2-$l^{3}-oxidanyl-1,3,2$l^{4}-dioxaborinan-2-yl]phenyl]propanal" _pdbx_chem_comp_synonyms.provenance PDB _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 SD0 "Create component" 2023-08-30 PDBE SD0 "Modify backbone" 2023-11-03 PDBE SD0 "Initial release" 2024-05-01 RCSB SD0 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id SD0 _pdbx_chem_comp_pcm.modified_residue_id PHE _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Non-standard residue" _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 ? _pdbx_chem_comp_pcm.modified_residue_id_linking_atom ? _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #