data_ORD # _chem_comp.id ORD _chem_comp.name D-ORNITHINE _chem_comp.type "D-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C5 H12 N2 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-09-08 _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 132.161 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ORD _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 1DSR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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 ORD N N N 0 1 N N N Y Y N 21.260 24.134 16.013 -0.758 1.774 0.274 N ORD 1 ORD CA CA C 0 1 N N R Y N N 22.332 23.116 15.912 -0.782 0.321 0.488 CA ORD 2 ORD CB CB C 0 1 N N N N N N 23.067 23.216 14.545 0.368 -0.327 -0.286 CB ORD 3 ORD CG CG C 0 1 N N N N N N 23.847 24.521 14.261 1.703 0.146 0.294 CG ORD 4 ORD CD CD C 0 1 N N N N N N 24.468 24.535 12.855 2.853 -0.502 -0.479 CD ORD 5 ORD NE NE N 0 1 N N N N N N 25.091 25.853 12.605 4.135 -0.049 0.078 NE ORD 6 ORD O O O 0 1 N N N Y N Y 20.797 21.414 15.164 -2.762 0.392 -0.787 O ORD 7 ORD OXT OXT O 0 1 N Y N Y N Y 22.101 20.852 16.914 -2.518 -1.434 0.435 OXT ORD 8 ORD C C C 0 1 N N N Y N Y 21.664 21.719 15.988 -2.093 -0.237 -0.002 C ORD 9 ORD H H H 0 1 N N N Y Y N 21.107 24.363 16.974 -0.860 1.997 -0.705 H ORD 10 ORD H2 H2 H 0 1 N Y N Y Y N 21.533 24.956 15.514 -1.468 2.232 0.825 H2 ORD 11 ORD HA HA H 0 1 N N N Y N N 23.058 23.275 16.723 -0.670 0.108 1.551 HA ORD 12 ORD HB2 HB2 H 0 1 N N N N N N 23.794 22.392 14.509 0.299 -1.411 -0.200 HB2 ORD 13 ORD HB3 HB3 H 0 1 N N N N N N 22.272 23.182 13.785 0.307 -0.041 -1.336 HB3 ORD 14 ORD HG2 HG2 H 0 1 N N N N N N 23.152 25.369 14.345 1.773 1.230 0.208 HG2 ORD 15 ORD HG3 HG3 H 0 1 N N N N N N 24.665 24.592 14.993 1.765 -0.140 1.344 HG3 ORD 16 ORD HD2 HD2 H 0 1 N N N N N N 25.233 23.748 12.784 2.783 -1.587 -0.393 HD2 ORD 17 ORD HD3 HD3 H 0 1 N N N N N N 23.684 24.352 12.106 2.792 -0.217 -1.529 HD3 ORD 18 ORD HE1 HE1 H 0 1 N N N N N N 25.232 26.326 13.475 4.189 -0.245 1.066 HE1 ORD 19 ORD HE2 HE2 H 0 1 N N N N N N 25.972 25.724 12.150 4.911 -0.463 -0.416 HE2 ORD 20 ORD HXT HXT H 0 1 N Y N Y N Y 21.645 20.025 16.814 -3.365 -1.750 0.093 HXT ORD 21 # 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 ORD N CA SING N N 1 ORD CA CB SING N N 2 ORD CA C SING N N 3 ORD CB CG SING N N 4 ORD CG CD SING N N 5 ORD CD NE SING N N 6 ORD C O DOUB N N 7 ORD C OXT SING N N 8 ORD N H SING N N 9 ORD N H2 SING N N 10 ORD CA HA SING N N 11 ORD CB HB2 SING N N 12 ORD CB HB3 SING N N 13 ORD CG HG2 SING N N 14 ORD CG HG3 SING N N 15 ORD CD HD2 SING N N 16 ORD CD HD3 SING N N 17 ORD NE HE1 SING N N 18 ORD NE HE2 SING N N 19 ORD OXT HXT SING N N 20 # 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 ORD SMILES ACDLabs 10.04 "O=C(O)C(N)CCCN" ORD SMILES_CANONICAL CACTVS 3.352 "NCCC[C@@H](N)C(O)=O" ORD SMILES CACTVS 3.352 "NCCC[CH](N)C(O)=O" ORD SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C(C[C@H](C(=O)O)N)CN" ORD SMILES "OpenEye OEToolkits" 1.6.1 "C(CC(C(=O)O)N)CN" ORD InChI InChI 1.03 "InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1" ORD InChIKey InChI 1.03 AHLPHDHHMVZTML-SCSAIBSYSA-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 ORD "SYSTEMATIC NAME" ACDLabs 10.04 D-ornithine ORD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R)-2,5-diaminopentanoic 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 ORD "Create component" 2010-09-08 EBI ORD "Modify descriptor" 2011-06-04 RCSB ORD "Modify backbone" 2023-11-03 PDBE ORD "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id ORD _pdbx_chem_comp_pcm.modified_residue_id ? _pdbx_chem_comp_pcm.type Ornithine _pdbx_chem_comp_pcm.category "Named protein 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 ? _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 ? #