data_VDL # _chem_comp.id VDL _chem_comp.name "(2R,3R)-2,3-DIAMINOBUTANOIC ACID" _chem_comp.type "D-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C4 H10 N2 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "D-ERITHRO-2,3-DIAMINO-BUTYRIC ACID" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-07-16 _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 118.134 _chem_comp.one_letter_code X _chem_comp.three_letter_code VDL _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 1W3M _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 VDL N N N 0 1 N N N Y Y N 35.590 31.145 34.372 0.228 1.911 0.256 N VDL 1 VDL CA CA C 0 1 N N R Y N N 35.975 30.087 35.331 0.109 0.462 0.465 CA VDL 2 VDL CB CB C 0 1 N N R N N N 34.820 29.787 36.266 1.161 -0.263 -0.377 CB VDL 3 VDL CG1 CG1 C 0 1 N N N N N N 35.119 28.597 37.147 2.557 0.200 0.044 CG1 VDL 4 VDL C C C 0 1 N N N Y N Y 37.207 30.529 36.070 -1.267 0.006 0.051 C VDL 5 VDL OXT OXT O 0 1 N Y N Y N Y 37.203 31.591 36.709 -1.753 -1.159 0.507 OXT VDL 6 VDL O O O 0 1 N N N Y N Y 38.218 29.707 36.074 -1.932 0.689 -0.691 O VDL 7 VDL NG2 NG2 N 0 1 N N N N N N 34.454 30.986 37.120 1.042 -1.712 -0.168 NG2 VDL 8 VDL H HN1 H 0 1 N N N Y Y N 36.357 31.336 33.760 1.118 2.252 0.586 HN1 VDL 9 VDL H2 HN2 H 0 1 N Y N Y Y N 34.804 30.838 33.835 0.086 2.149 -0.714 HN2 VDL 10 VDL HA HA H 0 1 N N N Y N N 36.208 29.152 34.801 0.265 0.232 1.519 HA VDL 11 VDL HB HB H 0 1 N N N N N N 33.956 29.546 35.629 1.004 -0.034 -1.431 HB VDL 12 VDL HG11 HG11 H 0 0 N N N N N N 34.263 28.407 37.811 3.307 -0.316 -0.556 HG11 VDL 13 VDL HG12 HG12 H 0 0 N N N N N N 35.299 27.712 36.519 2.646 1.275 -0.111 HG12 VDL 14 VDL HG13 HG13 H 0 0 N N N N N N 36.013 28.805 37.753 2.714 -0.030 1.098 HG13 VDL 15 VDL HXT HXT H 0 1 N Y N Y N Y 38.027 31.685 37.173 -2.640 -1.409 0.213 HXT VDL 16 VDL HG21 HG21 H 0 0 N N N N N N 33.691 30.748 37.721 0.108 -2.032 -0.377 HG21 VDL 17 VDL HG22 HG22 H 0 0 N N N N N N 35.242 31.254 37.674 1.727 -2.214 -0.713 HG22 VDL 18 # 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 VDL N CA SING N N 1 VDL N H SING N N 2 VDL N H2 SING N N 3 VDL CA CB SING N N 4 VDL CA C SING N N 5 VDL CA HA SING N N 6 VDL CB CG1 SING N N 7 VDL CB NG2 SING N N 8 VDL CB HB SING N N 9 VDL CG1 HG11 SING N N 10 VDL CG1 HG12 SING N N 11 VDL CG1 HG13 SING N N 12 VDL C OXT SING N N 13 VDL C O DOUB N N 14 VDL OXT HXT SING N N 15 VDL NG2 HG21 SING N N 16 VDL NG2 HG22 SING N N 17 # 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 VDL SMILES ACDLabs 11.02 "O=C(O)C(N)C(N)C" VDL SMILES_CANONICAL CACTVS 3.352 "C[C@@H](N)[C@@H](N)C(O)=O" VDL SMILES CACTVS 3.352 "C[CH](N)[CH](N)C(O)=O" VDL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@H]([C@H](C(=O)O)N)N" VDL SMILES "OpenEye OEToolkits" 1.7.0 "CC(C(C(=O)O)N)N" VDL InChI InChI 1.03 "InChI=1S/C4H10N2O2/c1-2(5)3(6)4(7)8/h2-3H,5-6H2,1H3,(H,7,8)/t2-,3-/m1/s1" VDL InChIKey InChI 1.03 SXGMVGOVILIERA-PWNYCUMCSA-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 VDL "SYSTEMATIC NAME" ACDLabs 11.02 "(2R,3R)-2,3-diaminobutanoic acid" VDL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R,3R)-2,3-bis(azanyl)butanoic 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 VDL "Create component" 2004-07-16 PDBJ VDL "Modify descriptor" 2011-06-04 RCSB VDL "Modify synonyms" 2020-06-05 PDBE VDL "Modify backbone" 2023-11-03 PDBE VDL "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VDL _pdbx_chem_comp_synonyms.name "D-ERITHRO-2,3-DIAMINO-BUTYRIC ACID" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id VDL _pdbx_chem_comp_pcm.modified_residue_id ? _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 ? #