data_4D4 # _chem_comp.id 4D4 _chem_comp.name "(2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C6 H14 N4 O3" _chem_comp.mon_nstd_parent_comp_id ARG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-03-02 _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 190.200 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4D4 _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 4YBB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 4D4 C C C 0 1 N N N Y N Y -68.492 127.273 158.137 3.399 -0.194 0.220 C 4D4 1 4D4 O O O 0 1 N N N Y N Y -69.198 127.593 157.141 4.023 0.040 -0.787 O 4D4 2 4D4 CA CA C 0 1 N N S Y N N -67.318 126.337 157.994 2.138 0.574 0.521 CA 4D4 3 4D4 N N N 0 1 N N N Y Y N -67.420 125.602 156.779 2.132 1.826 -0.247 N 4D4 4 4D4 CB CB C 0 1 N N R N N N -66.069 127.191 158.020 0.922 -0.269 0.131 CB 4D4 5 4D4 OB OB O 0 1 N N N N N N -65.805 127.716 156.739 1.035 -0.664 -1.237 OB 4D4 6 4D4 CG CG C 0 1 N N N N N N -64.889 126.369 158.493 -0.353 0.556 0.319 CG 4D4 7 4D4 CD CD C 0 1 N N N N N N -63.653 126.842 157.772 -1.575 -0.324 0.049 CD 4D4 8 4D4 NE NE N 0 1 N N N N N N -62.576 125.953 158.042 -2.795 0.466 0.230 NE 4D4 9 4D4 CZ CZ C 0 1 N N N N N N -61.255 126.342 157.700 -4.026 -0.117 0.040 CZ 4D4 10 4D4 NH2 NH2 N 0 1 N N N N N N -61.026 127.618 157.096 -4.107 -1.372 -0.301 NH2 4D4 11 4D4 NH1 NH1 N 0 1 N N N N N N -60.255 125.525 157.947 -5.171 0.625 0.209 NH1 4D4 12 4D4 OXT O1 O 0 1 N Y N Y N Y -68.706 127.743 159.359 3.826 -1.142 1.069 O1 4D4 13 4D4 HA H1 H 0 1 N N N Y N N -67.300 125.650 158.853 2.096 0.800 1.587 H1 4D4 14 4D4 H2 H2 H 0 1 N Y N Y Y N -68.253 125.049 156.792 2.170 1.643 -1.238 H2 4D4 15 4D4 H H3 H 0 1 N N N Y Y N -67.454 126.237 156.007 1.327 2.389 -0.014 H3 4D4 16 4D4 H5 H5 H 0 1 N N N N N N -66.226 128.013 158.734 0.877 -1.156 0.763 H5 4D4 17 4D4 H6 H6 H 0 1 N N N N N N -65.019 128.249 156.771 1.080 0.076 -1.858 H6 4D4 18 4D4 H7 H7 H 0 1 N N N N N N -65.064 125.306 158.270 -0.394 0.932 1.342 H7 4D4 19 4D4 H8 H8 H 0 1 N N N N N N -64.758 126.499 159.577 -0.349 1.395 -0.376 H8 4D4 20 4D4 H9 H9 H 0 1 N N N N N N -63.390 127.852 158.119 -1.533 -0.700 -0.973 H9 4D4 21 4D4 H10 H10 H 0 1 N N N N N N -63.847 126.865 156.689 -1.579 -1.163 0.745 H10 4D4 22 4D4 H11 H11 H 0 1 N N N N N N -62.748 125.065 158.468 -2.735 1.401 0.483 H11 4D4 23 4D4 H12 H12 H 0 1 N N N N N N -61.875 128.131 156.972 -3.299 -1.895 -0.420 H12 4D4 24 4D4 H14 H14 H 0 1 N N N N N N -60.428 124.637 158.373 -5.111 1.559 0.463 H14 4D4 25 4D4 H15 H15 H 0 1 N N N N N N -59.321 125.792 157.709 -6.039 0.214 0.075 H15 4D4 26 4D4 HXT H16 H 0 1 N Y N Y N Y -69.450 128.334 159.346 4.638 -1.611 0.831 H16 4D4 27 # 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 4D4 OB CB SING N N 1 4D4 N CA SING N N 2 4D4 NH2 CZ DOUB N N 3 4D4 O C DOUB N N 4 4D4 CZ NH1 SING N N 5 4D4 CZ NE SING N N 6 4D4 CD NE SING N N 7 4D4 CD CG SING N N 8 4D4 CA CB SING N N 9 4D4 CA C SING N N 10 4D4 CB CG SING N N 11 4D4 C OXT SING N N 12 4D4 CA HA SING N N 13 4D4 N H2 SING N N 14 4D4 N H SING N N 15 4D4 CB H5 SING N N 16 4D4 OB H6 SING N N 17 4D4 CG H7 SING N N 18 4D4 CG H8 SING N N 19 4D4 CD H9 SING N N 20 4D4 CD H10 SING N N 21 4D4 NE H11 SING N N 22 4D4 NH2 H12 SING N N 23 4D4 NH1 H14 SING N N 24 4D4 NH1 H15 SING N N 25 4D4 OXT HXT SING N N 26 # 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 4D4 SMILES ACDLabs 12.01 "C(O)(=O)C(C(CCN/C(N)=N)O)N" 4D4 InChI InChI 1.03 "InChI=1S/C6H14N4O3/c7-4(5(12)13)3(11)1-2-10-6(8)9/h3-4,11H,1-2,7H2,(H,12,13)(H4,8,9,10)/t3-,4+/m1/s1" 4D4 InChIKey InChI 1.03 VIDUVSPOWYVZIC-DMTCNVIQSA-N 4D4 SMILES_CANONICAL CACTVS 3.385 "N[C@@H]([C@H](O)CCNC(N)=N)C(O)=O" 4D4 SMILES CACTVS 3.385 "N[CH]([CH](O)CCNC(N)=N)C(O)=O" 4D4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C(/N)\NCC[C@H]([C@@H](C(=O)O)N)O" 4D4 SMILES "OpenEye OEToolkits" 1.7.6 "C(CNC(=N)N)C(C(C(=O)O)N)O" # 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 4D4 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3R)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)" 4D4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S,3R)-2-azanyl-5-carbamimidamido-3-oxidanyl-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 4D4 "Create component" 2015-03-02 RCSB 4D4 "Initial release" 2015-03-18 RCSB 4D4 "Modify parent residue" 2016-05-02 RCSB 4D4 "Modify backbone" 2023-11-03 PDBE 4D4 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 4D4 _pdbx_chem_comp_pcm.modified_residue_id ARG _pdbx_chem_comp_pcm.type Hydroxylation _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 PTM-0476 _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession PTM-0498 #