data_3D2 # _chem_comp.id 3D2 _chem_comp.name "N~2~-[3-(pyridin-3-yl)benzyl]-L-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 3D2 _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 4U5U _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 3D2 C19 C1 C 0 1 Y N N -0.983 29.983 13.082 6.378 0.664 1.237 C19 3D2 1 3D2 C14 C2 C 0 1 Y N N -0.029 34.325 10.634 2.696 -2.283 -0.629 C14 3D2 2 3D2 C15 C3 C 0 1 Y N N 0.464 33.740 11.794 2.823 -0.922 -0.359 C15 3D2 3 3D2 C16 C4 C 0 1 Y N N 0.013 32.474 12.199 4.087 -0.390 0.208 C16 3D2 4 3D2 C17 C5 C 0 1 Y N N 0.604 31.803 13.264 5.159 -1.244 0.477 C17 3D2 5 3D2 C18 C6 C 0 1 Y N N 0.141 30.552 13.673 6.317 -0.698 1.005 C18 3D2 6 3D2 C13 C7 C 0 1 Y N N 0.410 35.591 10.250 1.520 -2.772 -1.161 C13 3D2 7 3D2 C12 C8 C 0 1 Y N N 1.273 36.343 11.048 0.469 -1.913 -1.428 C12 3D2 8 3D2 C11 C9 C 0 1 Y N N 1.729 35.796 12.238 0.589 -0.561 -1.161 C11 3D2 9 3D2 C22 C10 C 0 1 Y N N 1.296 34.512 12.603 1.759 -0.062 -0.624 C22 3D2 10 3D2 C10 C11 C 0 1 N N N 2.602 36.432 13.148 -0.560 0.369 -1.455 C10 3D2 11 3D2 N20 N1 N 0 1 Y N N -1.625 30.675 12.052 5.350 1.446 0.969 N20 3D2 12 3D2 C21 C12 C 0 1 Y N N -1.131 31.923 11.623 4.227 0.971 0.471 C21 3D2 13 3D2 N09 N2 N 0 1 N N N 3.642 37.475 12.870 -1.428 0.463 -0.274 N09 3D2 14 3D2 C03 C13 C 0 1 N N S 3.410 38.882 12.396 -2.561 1.363 -0.524 C03 3D2 15 3D2 C02 C14 C 0 1 N N N 2.254 39.563 13.166 -2.144 2.785 -0.251 C02 3D2 16 3D2 O23 O1 O 0 1 N N N 1.383 40.200 12.567 -1.013 3.025 0.116 O23 3D2 17 3D2 N01 N3 N 0 1 N N N 2.305 39.449 14.493 -3.027 3.790 -0.415 N01 3D2 18 3D2 C04 C15 C 0 1 N N N 3.231 39.215 10.901 -3.724 0.988 0.397 C04 3D2 19 3D2 C05 C16 C 0 1 N N N 4.528 38.882 10.160 -4.229 -0.411 0.036 C05 3D2 20 3D2 C06 C17 C 0 1 N N N 4.410 39.327 8.700 -5.392 -0.786 0.957 C06 3D2 21 3D2 C07 C18 C 0 1 N N N 4.175 40.849 8.674 -5.898 -2.184 0.595 C07 3D2 22 3D2 N08 N4 N 0 1 N N N 5.278 41.590 9.313 -7.014 -2.545 1.480 N08 3D2 23 3D2 H1 H1 H 0 1 N N N -1.352 29.024 13.414 7.279 1.093 1.649 H1 3D2 24 3D2 H2 H2 H 0 1 N N N -0.753 33.798 10.030 3.517 -2.954 -0.426 H2 3D2 25 3D2 H3 H3 H 0 1 N N N 1.435 32.258 13.783 5.087 -2.303 0.278 H3 3D2 26 3D2 H4 H4 H 0 1 N N N 0.660 30.020 14.456 7.163 -1.329 1.233 H4 3D2 27 3D2 H5 H5 H 0 1 N N N 0.073 36.001 9.309 1.421 -3.827 -1.370 H5 3D2 28 3D2 H6 H6 H 0 1 N N N 1.580 37.333 10.744 -0.449 -2.299 -1.845 H6 3D2 29 3D2 H7 H7 H 0 1 N N N 1.621 34.105 13.549 1.852 0.993 -0.417 H7 3D2 30 3D2 H8 H8 H 0 1 N N N 1.936 36.897 13.890 -0.173 1.357 -1.702 H8 3D2 31 3D2 H9 H9 H 0 1 N N N 3.157 35.608 13.620 -1.134 -0.018 -2.298 H9 3D2 32 3D2 H10 H10 H 0 1 N N N -1.645 32.459 10.839 3.407 1.644 0.264 H10 3D2 33 3D2 H11 H11 H 0 1 N N N 4.238 37.066 12.179 -0.904 0.758 0.537 H11 3D2 34 3D2 H13 H13 H 0 1 N N N 4.310 39.437 12.699 -2.876 1.270 -1.563 H13 3D2 35 3D2 H14 H14 H 0 1 N N N 1.612 39.894 15.060 -3.931 3.598 -0.708 H14 3D2 36 3D2 H15 H15 H 0 1 N N N 3.036 38.919 14.922 -2.758 4.706 -0.239 H15 3D2 37 3D2 H16 H16 H 0 1 N N N 3.004 40.285 10.786 -3.384 0.994 1.433 H16 3D2 38 3D2 H17 H17 H 0 1 N N N 2.405 38.618 10.486 -4.532 1.709 0.275 H17 3D2 39 3D2 H18 H18 H 0 1 N N N 4.705 37.797 10.200 -4.569 -0.417 -1.000 H18 3D2 40 3D2 H19 H19 H 0 1 N N N 5.368 39.408 10.637 -3.421 -1.132 0.157 H19 3D2 41 3D2 H20 H20 H 0 1 N N N 3.564 38.812 8.222 -5.052 -0.779 1.992 H20 3D2 42 3D2 H21 H21 H 0 1 N N N 5.338 39.085 8.162 -6.200 -0.065 0.835 H21 3D2 43 3D2 H22 H22 H 0 1 N N N 4.086 41.177 7.628 -6.238 -2.191 -0.440 H22 3D2 44 3D2 H23 H23 H 0 1 N N N 3.240 41.073 9.209 -5.089 -2.906 0.717 H23 3D2 45 3D2 H24 H24 H 0 1 N N N 5.087 42.571 9.275 -7.749 -1.856 1.433 H24 3D2 46 3D2 H25 H25 H 0 1 N N N 5.363 41.304 10.267 -7.365 -3.465 1.261 H25 3D2 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 3D2 C07 C06 SING N N 1 3D2 C07 N08 SING N N 2 3D2 C06 C05 SING N N 3 3D2 C05 C04 SING N N 4 3D2 C13 C14 DOUB Y N 5 3D2 C13 C12 SING Y N 6 3D2 C14 C15 SING Y N 7 3D2 C04 C03 SING N N 8 3D2 C12 C11 DOUB Y N 9 3D2 C21 N20 DOUB Y N 10 3D2 C21 C16 SING Y N 11 3D2 C15 C16 SING N N 12 3D2 C15 C22 DOUB Y N 13 3D2 N20 C19 SING Y N 14 3D2 C16 C17 DOUB Y N 15 3D2 C11 C22 SING Y N 16 3D2 C11 C10 SING N N 17 3D2 C03 N09 SING N N 18 3D2 C03 C02 SING N N 19 3D2 O23 C02 DOUB N N 20 3D2 N09 C10 SING N N 21 3D2 C19 C18 DOUB Y N 22 3D2 C02 N01 SING N N 23 3D2 C17 C18 SING Y N 24 3D2 C19 H1 SING N N 25 3D2 C14 H2 SING N N 26 3D2 C17 H3 SING N N 27 3D2 C18 H4 SING N N 28 3D2 C13 H5 SING N N 29 3D2 C12 H6 SING N N 30 3D2 C22 H7 SING N N 31 3D2 C10 H8 SING N N 32 3D2 C10 H9 SING N N 33 3D2 C21 H10 SING N N 34 3D2 N09 H11 SING N N 35 3D2 C03 H13 SING N N 36 3D2 N01 H14 SING N N 37 3D2 N01 H15 SING N N 38 3D2 C04 H16 SING N N 39 3D2 C04 H17 SING N N 40 3D2 C05 H18 SING N N 41 3D2 C05 H19 SING N N 42 3D2 C06 H20 SING N N 43 3D2 C06 H21 SING N N 44 3D2 C07 H22 SING N N 45 3D2 C07 H23 SING N N 46 3D2 N08 H24 SING N N 47 3D2 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 3D2 SMILES ACDLabs 12.01 "O=C(N)C(NCc2cc(c1cccnc1)ccc2)CCCCN" 3D2 InChI InChI 1.03 "InChI=1S/C18H24N4O/c19-9-2-1-8-17(18(20)23)22-12-14-5-3-6-15(11-14)16-7-4-10-21-13-16/h3-7,10-11,13,17,22H,1-2,8-9,12,19H2,(H2,20,23)/t17-/m0/s1" 3D2 InChIKey InChI 1.03 HSVQHUWOLRPWEF-KRWDZBQOSA-N 3D2 SMILES_CANONICAL CACTVS 3.385 "NCCCC[C@H](NCc1cccc(c1)c2cccnc2)C(N)=O" 3D2 SMILES CACTVS 3.385 "NCCCC[CH](NCc1cccc(c1)c2cccnc2)C(N)=O" 3D2 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1cc(cc(c1)c2cccnc2)CN[C@@H](CCCCN)C(=O)N" 3D2 SMILES "OpenEye OEToolkits" 1.9.2 "c1cc(cc(c1)c2cccnc2)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 3D2 "SYSTEMATIC NAME" ACDLabs 12.01 "N~2~-[3-(pyridin-3-yl)benzyl]-L-lysinamide" 3D2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S)-6-azanyl-2-[(3-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 3D2 "Create component" 2014-07-28 EBI 3D2 "Modify descriptor" 2014-09-05 RCSB 3D2 "Initial release" 2015-05-13 RCSB #