data_2YJ # _chem_comp.id 2YJ _chem_comp.name N~5~-D-lysyl-L-ornithine _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C11 H24 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-04-14 _chem_comp.pdbx_modified_date 2014-04-18 _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 260.333 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2YJ _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 4Q3E _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 2YJ O2 O2 O 0 1 N N N -10.249 -33.891 20.631 6.412 -1.243 0.876 O2 2YJ 1 2YJ C10 C10 C 0 1 N N N -9.362 -33.243 21.186 5.931 -0.575 -0.008 C10 2YJ 2 2YJ O1 O1 O 0 1 N Y N -9.280 -33.266 22.514 6.651 0.404 -0.578 O1 2YJ 3 2YJ C C C 0 1 N N S -8.354 -32.411 20.429 4.523 -0.845 -0.475 C 2YJ 4 2YJ N N N 0 1 N N N -7.894 -33.094 19.234 4.129 -2.205 -0.082 N 2YJ 5 2YJ C1 C1 C 0 1 N N N -9.024 -31.088 20.082 3.571 0.167 0.164 C1 2YJ 6 2YJ C2 C2 C 0 1 N N N -8.134 -30.063 19.376 2.164 -0.027 -0.405 C2 2YJ 7 2YJ C3 C3 C 0 1 N N N -8.994 -28.814 19.205 1.211 0.985 0.234 C3 2YJ 8 2YJ N1 N1 N 0 1 N N N -8.438 -27.744 18.396 -0.136 0.799 -0.311 N1 2YJ 9 2YJ C4 C4 C 0 1 N N N -7.700 -26.775 18.932 -1.147 1.586 0.109 C4 2YJ 10 2YJ O O O 0 1 N N N -7.340 -26.801 20.096 -0.942 2.447 0.938 O 2YJ 11 2YJ C5 C5 C 0 1 N N R -7.344 -25.599 18.061 -2.533 1.394 -0.451 C5 2YJ 12 2YJ N3 N3 N 0 1 N N N -5.905 -25.428 18.081 -3.322 2.613 -0.231 N3 2YJ 13 2YJ C6 C6 C 0 1 N N N -8.002 -24.318 18.583 -3.209 0.215 0.251 C6 2YJ 14 2YJ C7 C7 C 0 1 N N N -9.465 -24.173 18.170 -4.565 -0.058 -0.402 C7 2YJ 15 2YJ C8 C8 C 0 1 N N N -9.928 -22.719 18.274 -5.241 -1.237 0.300 C8 2YJ 16 2YJ C9 C9 C 0 1 N N N -10.172 -22.273 19.718 -6.598 -1.510 -0.353 C9 2YJ 17 2YJ N2 N2 N 0 1 N N N -9.402 -21.079 20.028 -7.247 -2.643 0.322 N2 2YJ 18 2YJ H1 H1 H 0 1 N Y N -9.968 -33.819 22.865 7.550 0.537 -0.248 H1 2YJ 19 2YJ H2 H2 H 0 1 N N N -7.498 -32.207 21.089 4.477 -0.753 -1.561 H2 2YJ 20 2YJ H3 H3 H 0 1 N N N -7.459 -33.957 19.490 4.164 -2.316 0.920 H3 2YJ 21 2YJ H4 H4 H 0 1 N N N -8.673 -33.278 18.635 3.214 -2.433 -0.439 H4 2YJ 22 2YJ H6 H6 H 0 1 N N N -9.385 -30.636 21.017 3.550 0.016 1.243 H6 2YJ 23 2YJ H7 H7 H 0 1 N N N -9.879 -31.304 19.425 3.915 1.178 -0.055 H7 2YJ 24 2YJ H8 H8 H 0 1 N N N -7.814 -30.445 18.395 2.184 0.124 -1.484 H8 2YJ 25 2YJ H9 H9 H 0 1 N N N -7.249 -29.838 19.989 1.820 -1.038 -0.187 H9 2YJ 26 2YJ H10 H10 H 0 1 N N N -9.191 -28.406 20.207 1.191 0.834 1.313 H10 2YJ 27 2YJ H11 H11 H 0 1 N N N -9.942 -29.123 18.742 1.555 1.996 0.015 H11 2YJ 28 2YJ H12 H12 H 0 1 N N N -8.614 -27.735 17.412 -0.300 0.111 -0.974 H12 2YJ 29 2YJ H13 H13 H 0 1 N N N -7.690 -25.787 17.034 -2.468 1.192 -1.520 H13 2YJ 30 2YJ H14 H14 H 0 1 N N N -5.465 -26.260 17.742 -4.235 2.534 -0.655 H14 2YJ 31 2YJ H15 H15 H 0 1 N N N -5.653 -24.656 17.497 -3.398 2.823 0.753 H15 2YJ 32 2YJ H17 H17 H 0 1 N N N -7.949 -24.322 19.682 -2.579 -0.670 0.163 H17 2YJ 33 2YJ H18 H18 H 0 1 N N N -7.443 -23.455 18.192 -3.354 0.454 1.304 H18 2YJ 34 2YJ H19 H19 H 0 1 N N N -10.087 -24.796 18.830 -5.195 0.827 -0.314 H19 2YJ 35 2YJ H20 H20 H 0 1 N N N -9.579 -24.512 17.130 -4.420 -0.297 -1.455 H20 2YJ 36 2YJ H21 H21 H 0 1 N N N -9.155 -22.072 17.833 -4.611 -2.122 0.212 H21 2YJ 37 2YJ H22 H22 H 0 1 N N N -10.865 -22.608 17.709 -5.386 -0.998 1.354 H22 2YJ 38 2YJ H23 H23 H 0 1 N N N -11.242 -22.057 19.852 -7.228 -0.626 -0.265 H23 2YJ 39 2YJ H24 H24 H 0 1 N N N -9.873 -23.082 20.401 -6.452 -1.750 -1.406 H24 2YJ 40 2YJ H25 H25 H 0 1 N N N -9.576 -20.806 20.974 -8.145 -2.843 -0.092 H25 2YJ 41 2YJ H26 H26 H 0 1 N N N -8.428 -21.271 19.911 -6.653 -3.459 0.310 H26 2YJ 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 2YJ C5 N3 SING N N 1 2YJ C5 C6 SING N N 2 2YJ C5 C4 SING N N 3 2YJ C7 C8 SING N N 4 2YJ C7 C6 SING N N 5 2YJ C8 C9 SING N N 6 2YJ N1 C4 SING N N 7 2YJ N1 C3 SING N N 8 2YJ C4 O DOUB N N 9 2YJ C3 C2 SING N N 10 2YJ N C SING N N 11 2YJ C2 C1 SING N N 12 2YJ C9 N2 SING N N 13 2YJ C1 C SING N N 14 2YJ C C10 SING N N 15 2YJ O2 C10 DOUB N N 16 2YJ C10 O1 SING N N 17 2YJ O1 H1 SING N N 18 2YJ C H2 SING N N 19 2YJ N H3 SING N N 20 2YJ N H4 SING N N 21 2YJ C1 H6 SING N N 22 2YJ C1 H7 SING N N 23 2YJ C2 H8 SING N N 24 2YJ C2 H9 SING N N 25 2YJ C3 H10 SING N N 26 2YJ C3 H11 SING N N 27 2YJ N1 H12 SING N N 28 2YJ C5 H13 SING N N 29 2YJ N3 H14 SING N N 30 2YJ N3 H15 SING N N 31 2YJ C6 H17 SING N N 32 2YJ C6 H18 SING N N 33 2YJ C7 H19 SING N N 34 2YJ C7 H20 SING N N 35 2YJ C8 H21 SING N N 36 2YJ C8 H22 SING N N 37 2YJ C9 H23 SING N N 38 2YJ C9 H24 SING N N 39 2YJ N2 H25 SING N N 40 2YJ N2 H26 SING N N 41 # 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 2YJ SMILES ACDLabs 12.01 "O=C(O)C(N)CCCNC(=O)C(N)CCCCN" 2YJ InChI InChI 1.03 "InChI=1S/C11H24N4O3/c12-6-2-1-4-8(13)10(16)15-7-3-5-9(14)11(17)18/h8-9H,1-7,12-14H2,(H,15,16)(H,17,18)/t8-,9+/m1/s1" 2YJ InChIKey InChI 1.03 IIZZYHGWMHUAMZ-BDAKNGLRSA-N 2YJ SMILES_CANONICAL CACTVS 3.385 "NCCCC[C@@H](N)C(=O)NCCC[C@H](N)C(O)=O" 2YJ SMILES CACTVS 3.385 "NCCCC[CH](N)C(=O)NCCC[CH](N)C(O)=O" 2YJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(CCN)C[C@H](C(=O)NCCC[C@@H](C(=O)O)N)N" 2YJ SMILES "OpenEye OEToolkits" 1.7.6 "C(CCN)CC(C(=O)NCCCC(C(=O)O)N)N" # 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 2YJ "SYSTEMATIC NAME" ACDLabs 12.01 N~5~-D-lysyl-L-ornithine 2YJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-5-[[(2R)-2,6-bis(azanyl)hexanoyl]amino]pentanoic 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 2YJ "Create component" 2014-04-14 RCSB 2YJ "Initial release" 2014-04-23 RCSB #