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 
# 
