data_A1DEJ # _chem_comp.id A1DEJ _chem_comp.name "(2~{S})-2-azanyl-5-(3-methylbenzimidazol-1-yl)pentanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H18 N3 O2" _chem_comp.mon_nstd_parent_comp_id ALA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2026-04-23 _chem_comp.pdbx_modified_date 2026-09-18 _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 248.301 _chem_comp.one_letter_code A _chem_comp.three_letter_code A1DEJ _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 Y _chem_comp.pdbx_model_coordinates_db_code 12YU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y _chem_comp.pdbx_comp_type ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1DEJ N N1 N 0 1 N N N Y Y N 33.849 -6.170 1.662 ? ? ? N A1DEJ 1 A1DEJ CA C1 C 0 1 N N S N Y N 35.225 -5.713 1.657 ? ? ? CA A1DEJ 2 A1DEJ C C2 C 0 1 N N N N Y Y 35.231 -4.195 1.677 ? ? ? C A1DEJ 3 A1DEJ O O1 O 0 1 N N N N Y Y 34.636 -3.570 0.810 ? ? ? O A1DEJ 4 A1DEJ CB C3 C 0 1 N N N N N N 35.970 -6.273 0.435 ? ? ? CB A1DEJ 5 A1DEJ CG C4 C 0 1 N N N N N N 35.941 -7.815 0.522 ? ? ? CG A1DEJ 6 A1DEJ CD C5 C 0 1 N N N N N N 36.189 -8.472 -0.825 ? ? ? CD A1DEJ 7 A1DEJ NE N2 N 0 1 Y N N N N N 37.472 -8.105 -1.402 ? ? ? NE A1DEJ 8 A1DEJ CZ1 C6 C 0 1 Y N N N N N 38.692 -8.525 -1.008 ? ? ? CZ1 A1DEJ 9 A1DEJ CZ2 C7 C 0 1 Y N N N N N 37.667 -7.240 -2.441 ? ? ? CZ2 A1DEJ 10 A1DEJ NH1 N3 N 1 1 Y N N N N N 39.624 -7.970 -1.792 ? ? ? NH1 A1DEJ 11 A1DEJ CH2 C8 C 0 1 Y N N N N N 39.025 -7.145 -2.694 ? ? ? CH2 A1DEJ 12 A1DEJ CH3 C9 C 0 1 Y N N N N N 36.773 -6.496 -3.275 ? ? ? CH3 A1DEJ 13 A1DEJ CI2 C10 C 0 1 Y N N N N N 38.670 -5.591 -4.523 ? ? ? CI2 A1DEJ 14 A1DEJ CT1 C11 C 0 1 N N N N N N 41.055 -8.126 -1.713 ? ? ? CT1 A1DEJ 15 A1DEJ CT2 C12 C 0 1 Y N N N N N 39.554 -6.324 -3.727 ? ? ? CT2 A1DEJ 16 A1DEJ CT3 C13 C 0 1 Y N N N N N 37.313 -5.706 -4.271 ? ? ? CT3 A1DEJ 17 A1DEJ H H1 H 0 1 N N N Y Y N 33.377 -5.799 2.461 ? ? ? H A1DEJ 18 A1DEJ H2 H2 H 0 1 N N N Y Y N 33.391 -5.858 0.830 ? ? ? H2 A1DEJ 19 A1DEJ HA H4 H 0 1 N N N N Y N 35.732 -6.075 2.564 ? ? ? HA A1DEJ 20 A1DEJ HB1 H6 H 0 1 N N N N N N 37.011 -5.919 0.438 ? ? ? HB1 A1DEJ 21 A1DEJ HB2 H7 H 0 1 N N N N N N 35.473 -5.942 -0.489 ? ? ? HB2 A1DEJ 22 A1DEJ H8 H8 H 0 1 N N N N N N 34.955 -8.130 0.893 ? ? ? H8 A1DEJ 23 A1DEJ H9 H9 H 0 1 N N N N N N 36.720 -8.145 1.225 ? ? ? H9 A1DEJ 24 A1DEJ H10 H10 H 0 1 N N N N N N 35.391 -8.166 -1.518 ? ? ? H10 A1DEJ 25 A1DEJ H11 H11 H 0 1 N N N N N N 36.162 -9.564 -0.694 ? ? ? H11 A1DEJ 26 A1DEJ H12 H12 H 0 1 N N N N N N 38.886 -9.202 -0.189 ? ? ? H12 A1DEJ 27 A1DEJ H13 H13 H 0 1 N N N N N N 35.704 -6.551 -3.129 ? ? ? H13 A1DEJ 28 A1DEJ H14 H14 H 0 1 N N N N N N 39.035 -4.952 -5.313 ? ? ? H14 A1DEJ 29 A1DEJ H15 H15 H 0 1 N N N N N N 41.303 -8.840 -0.914 ? ? ? H15 A1DEJ 30 A1DEJ H16 H16 H 0 1 N N N N N N 41.436 -8.504 -2.673 ? ? ? H16 A1DEJ 31 A1DEJ H17 H17 H 0 1 N N N N N N 41.518 -7.153 -1.492 ? ? ? H17 A1DEJ 32 A1DEJ H18 H18 H 0 1 N N N N N N 40.620 -6.268 -3.893 ? ? ? H18 A1DEJ 33 A1DEJ H19 H19 H 0 1 N N N N N N 36.634 -5.142 -4.893 ? ? ? H19 A1DEJ 34 A1DEJ OXT OXT O 0 1 N N N N Y Y 35.901 -3.617 2.677 ? ? ? OXT A1DEJ 35 A1DEJ H1 H1 H 0 1 N N N N N N 35.836 -2.673 2.598 ? ? ? H1 A1DEJ 36 # 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 A1DEJ CI2 CT3 DOUB Y N 1 A1DEJ CI2 CT2 SING Y N 2 A1DEJ CT3 CH3 SING Y N 3 A1DEJ CT2 CH2 DOUB Y N 4 A1DEJ CH3 CZ2 DOUB Y N 5 A1DEJ CH2 CZ2 SING Y N 6 A1DEJ CH2 NH1 SING Y N 7 A1DEJ CZ2 NE SING Y N 8 A1DEJ NH1 CT1 SING N N 9 A1DEJ NH1 CZ1 DOUB Y N 10 A1DEJ NE CZ1 SING Y N 11 A1DEJ NE CD SING N N 12 A1DEJ CD CG SING N N 13 A1DEJ CB CG SING N N 14 A1DEJ CB CA SING N N 15 A1DEJ O C DOUB N N 16 A1DEJ CA N SING N N 17 A1DEJ CA C SING N N 18 A1DEJ N H SING N N 19 A1DEJ N H2 SING N N 20 A1DEJ CA HA SING N N 21 A1DEJ CB HB1 SING N N 22 A1DEJ CB HB2 SING N N 23 A1DEJ CG H8 SING N N 24 A1DEJ CG H9 SING N N 25 A1DEJ CD H10 SING N N 26 A1DEJ CD H11 SING N N 27 A1DEJ CZ1 H12 SING N N 28 A1DEJ CH3 H13 SING N N 29 A1DEJ CI2 H14 SING N N 30 A1DEJ CT1 H15 SING N N 31 A1DEJ CT1 H16 SING N N 32 A1DEJ CT1 H17 SING N N 33 A1DEJ CT2 H18 SING N N 34 A1DEJ CT3 H19 SING N N 35 A1DEJ C OXT SING N N 36 A1DEJ OXT H1 SING N N 37 # 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 A1DEJ InChI InChI 1.06 "InChI=1S/C13H18N3O2/c1-15-9-16(8-4-5-10(14)13(17)18)12-7-3-2-6-11(12)15/h2-3,6-7,9-10H,4-5,8,14H2,1H3,(H,17,18)/t10-/m0/s1" A1DEJ InChIKey InChI 1.06 OFSPGMNGABDJOI-JTQLQIEISA-N A1DEJ SMILES_CANONICAL CACTVS 3.385 "C[n]1cn(CCC[C@H](N)C(O)=O)c2ccccc12" A1DEJ SMILES CACTVS 3.385 "C[n]1cn(CCC[CH](N)C(O)=O)c2ccccc12" A1DEJ SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[N]1=CN(c2c1cccc2)CCC[C@@H](C(=O)O)N" A1DEJ SMILES "OpenEye OEToolkits" 3.1.0.0 "C[N]1=CN(c2c1cccc2)CCCC(C(=O)O)N" # _pdbx_chem_comp_identifier.comp_id A1DEJ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "(2~{S})-2-azanyl-5-(3-methylbenzimidazol-1-yl)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 A1DEJ "Create component" 2026-04-23 RCSB A1DEJ "Initial release" 2026-09-23 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1DEJ _pdbx_chem_comp_pcm.modified_residue_id ALA _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 ? #