data_3D5 # _chem_comp.id 3D5 _chem_comp.name "N~2~-[4-(pyridin-3-yl)benzyl]-D-lysinamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H24 N4 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-28 _chem_comp.pdbx_modified_date 2015-05-08 _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 312.409 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3D5 _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 4U5O _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 3D5 C18 C1 C 0 1 Y N N 0.523 31.468 13.424 -5.307 0.537 0.796 C18 3D5 1 3D5 C19 C2 C 0 1 Y N N 0.098 30.215 13.841 -6.600 0.108 1.046 C19 3D5 2 3D5 C20 C3 C 0 1 Y N N -1.032 29.653 13.260 -7.012 -1.119 0.559 C20 3D5 3 3D5 N21 N1 N 0 1 Y N N -1.703 30.351 12.245 -6.193 -1.884 -0.137 N21 3D5 4 3D5 C22 C4 C 0 1 Y N N -1.263 31.601 11.810 -4.955 -1.519 -0.399 C22 3D5 5 3D5 C17 C5 C 0 1 Y N N -0.118 32.137 12.387 -4.466 -0.294 0.051 C17 3D5 6 3D5 C16 C6 C 0 1 Y N N 0.323 33.396 12.012 -3.071 0.117 -0.246 C16 3D5 7 3D5 C15 C7 C 0 1 Y N N -0.133 33.976 10.832 -2.590 1.341 0.213 C15 3D5 8 3D5 C14 C8 C 0 1 Y N N 0.353 35.222 10.441 -1.292 1.718 -0.065 C14 3D5 9 3D5 C13 C9 C 0 1 Y N N 1.311 34.015 12.762 -2.236 -0.723 -0.980 C13 3D5 10 3D5 C12 C10 C 0 1 Y N N 1.777 35.267 12.395 -0.940 -0.337 -1.252 C12 3D5 11 3D5 C11 C11 C 0 1 Y N N 1.306 35.858 11.230 -0.469 0.882 -0.799 C11 3D5 12 3D5 C10 C12 C 0 1 N N N 1.796 37.097 10.876 0.948 1.299 -1.100 C10 3D5 13 3D5 N09 N2 N 0 1 N N N 2.791 37.015 9.797 1.835 0.828 -0.028 N09 3D5 14 3D5 C03 C13 C 0 1 N N R 3.230 38.403 9.589 3.228 1.217 -0.289 C03 3D5 15 3D5 C02 C14 C 0 1 N N N 3.798 38.951 10.920 3.462 2.616 0.220 C02 3D5 16 3D5 O23 O1 O 0 1 N N N 3.242 39.880 11.511 2.558 3.229 0.747 O23 3D5 17 3D5 N01 N3 N 0 1 N N N 4.885 38.324 11.382 4.676 3.187 0.088 N01 3D5 18 3D5 C04 C15 C 0 1 N N N 4.248 38.489 8.450 4.170 0.249 0.429 C04 3D5 19 3D5 C05 C16 C 0 1 N N N 3.593 37.970 7.155 4.021 -1.149 -0.174 C05 3D5 20 3D5 C06 C17 C 0 1 N N N 2.356 38.793 6.741 4.964 -2.117 0.544 C06 3D5 21 3D5 C07 C18 C 0 1 N N N 1.800 38.192 5.435 4.815 -3.515 -0.059 C07 3D5 22 3D5 N08 N4 N 0 1 N N N 0.615 38.900 4.903 5.720 -4.445 0.630 N08 3D5 23 3D5 H1 H1 H 0 1 N N N 1.367 31.932 13.913 -4.959 1.491 1.164 H1 3D5 24 3D5 H2 H2 H 0 1 N N N 0.640 29.682 14.609 -7.279 0.726 1.614 H2 3D5 25 3D5 H3 H3 H 0 1 N N N -1.390 28.688 13.587 -8.019 -1.456 0.752 H3 3D5 26 3D5 H4 H4 H 0 1 N N N -1.799 32.140 11.043 -4.314 -2.172 -0.972 H4 3D5 27 3D5 H5 H5 H 0 1 N N N -0.861 33.462 10.222 -3.232 1.995 0.785 H5 3D5 28 3D5 H6 H6 H 0 1 N N N -0.006 35.689 9.536 -0.918 2.667 0.289 H6 3D5 29 3D5 H7 H7 H 0 1 N N N 1.717 33.521 13.632 -2.603 -1.675 -1.334 H7 3D5 30 3D5 H8 H8 H 0 1 N N N 2.501 35.780 13.011 -0.292 -0.987 -1.821 H8 3D5 31 3D5 H9 H9 H 0 1 N N N 2.267 37.556 11.758 1.261 0.863 -2.049 H9 3D5 32 3D5 H10 H10 H 0 1 N N N 0.959 37.725 10.538 1.001 2.386 -1.165 H10 3D5 33 3D5 H11 H11 H 0 1 N N N 2.378 36.647 8.964 1.756 -0.170 0.095 H11 3D5 34 3D5 H13 H13 H 0 1 N N N 2.358 39.015 9.316 3.420 1.184 -1.361 H13 3D5 35 3D5 H14 H14 H 0 1 N N N 5.291 38.603 12.252 5.399 2.697 -0.334 H14 3D5 36 3D5 H15 H15 H 0 1 N N N 5.292 37.576 10.857 4.827 4.087 0.415 H15 3D5 37 3D5 H16 H16 H 0 1 N N N 5.126 37.873 8.692 5.199 0.589 0.309 H16 3D5 38 3D5 H17 H17 H 0 1 N N N 4.561 39.535 8.312 3.919 0.217 1.489 H17 3D5 39 3D5 H18 H18 H 0 1 N N N 3.285 36.926 7.311 2.992 -1.488 -0.054 H18 3D5 40 3D5 H19 H19 H 0 1 N N N 4.334 38.016 6.343 4.272 -1.116 -1.234 H19 3D5 41 3D5 H20 H20 H 0 1 N N N 2.643 39.842 6.577 5.993 -1.778 0.424 H20 3D5 42 3D5 H21 H21 H 0 1 N N N 1.592 38.742 7.531 4.713 -2.150 1.604 H21 3D5 43 3D5 H22 H22 H 0 1 N N N 1.520 37.146 5.627 3.786 -3.855 0.060 H22 3D5 44 3D5 H23 H23 H 0 1 N N N 2.593 38.225 4.674 5.066 -3.483 -1.119 H23 3D5 45 3D5 H24 H24 H 0 1 N N N 0.312 38.456 4.060 5.640 -5.376 0.250 H24 3D5 46 3D5 H25 H25 H 0 1 N N N -0.122 38.871 5.578 6.674 -4.118 0.589 H25 3D5 47 # 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 3D5 N08 C07 SING N N 1 3D5 C07 C06 SING N N 2 3D5 C06 C05 SING N N 3 3D5 C05 C04 SING N N 4 3D5 C04 C03 SING N N 5 3D5 C03 N09 SING N N 6 3D5 C03 C02 SING N N 7 3D5 N09 C10 SING N N 8 3D5 C14 C15 DOUB Y N 9 3D5 C14 C11 SING Y N 10 3D5 C15 C16 SING Y N 11 3D5 C10 C11 SING N N 12 3D5 C02 N01 SING N N 13 3D5 C02 O23 DOUB N N 14 3D5 C11 C12 DOUB Y N 15 3D5 C22 N21 DOUB Y N 16 3D5 C22 C17 SING Y N 17 3D5 C16 C17 SING N N 18 3D5 C16 C13 DOUB Y N 19 3D5 N21 C20 SING Y N 20 3D5 C17 C18 DOUB Y N 21 3D5 C12 C13 SING Y N 22 3D5 C20 C19 DOUB Y N 23 3D5 C18 C19 SING Y N 24 3D5 C18 H1 SING N N 25 3D5 C19 H2 SING N N 26 3D5 C20 H3 SING N N 27 3D5 C22 H4 SING N N 28 3D5 C15 H5 SING N N 29 3D5 C14 H6 SING N N 30 3D5 C13 H7 SING N N 31 3D5 C12 H8 SING N N 32 3D5 C10 H9 SING N N 33 3D5 C10 H10 SING N N 34 3D5 N09 H11 SING N N 35 3D5 C03 H13 SING N N 36 3D5 N01 H14 SING N N 37 3D5 N01 H15 SING N N 38 3D5 C04 H16 SING N N 39 3D5 C04 H17 SING N N 40 3D5 C05 H18 SING N N 41 3D5 C05 H19 SING N N 42 3D5 C06 H20 SING N N 43 3D5 C06 H21 SING N N 44 3D5 C07 H22 SING N N 45 3D5 C07 H23 SING N N 46 3D5 N08 H24 SING N N 47 3D5 N08 H25 SING N N 48 # 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 3D5 SMILES ACDLabs 12.01 "O=C(N)C(NCc2ccc(c1cccnc1)cc2)CCCCN" 3D5 InChI InChI 1.03 "InChI=1S/C18H24N4O/c19-10-2-1-5-17(18(20)23)22-12-14-6-8-15(9-7-14)16-4-3-11-21-13-16/h3-4,6-9,11,13,17,22H,1-2,5,10,12,19H2,(H2,20,23)/t17-/m1/s1" 3D5 InChIKey InChI 1.03 KSWNFCZKQDWGEE-QGZVFWFLSA-N 3D5 SMILES_CANONICAL CACTVS 3.385 "NCCCC[C@@H](NCc1ccc(cc1)c2cccnc2)C(N)=O" 3D5 SMILES CACTVS 3.385 "NCCCC[CH](NCc1ccc(cc1)c2cccnc2)C(N)=O" 3D5 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1cc(cnc1)c2ccc(cc2)CN[C@H](CCCCN)C(=O)N" 3D5 SMILES "OpenEye OEToolkits" 1.9.2 "c1cc(cnc1)c2ccc(cc2)CNC(CCCCN)C(=O)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 3D5 "SYSTEMATIC NAME" ACDLabs 12.01 "N~2~-[4-(pyridin-3-yl)benzyl]-D-lysinamide" 3D5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2R)-6-azanyl-2-[(4-pyridin-3-ylphenyl)methylamino]hexanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3D5 "Other modification" 2014-07-28 RCSB 3D5 "Modify descriptor" 2014-09-05 RCSB 3D5 "Initial release" 2015-05-13 RCSB #