data_4CDD # _model_server_result.job_id xCTfZP1eDLJ8BXPk8wqLzg _model_server_result.datetime_utc '2025-03-04 15:30:42' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4cdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1369}' # _entry.id 4CDD # _exptl.entry_id 4CDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.452 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]PIPERIDINE-2-CARBOXAMIDE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4CDD _cell.length_a 84.291 _cell.length_b 84.291 _cell.length_c 221.114 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 software_defined_assembly 1 PISA trimeric 3 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression D,E,F,L,M,N,R,S 1 1 A,B,C,G,H,I,J,K,O,P,Q 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 J N N ? 6 M N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n G NAG 1 G 1 NAG A 1120 NAG 4 n G NAG 2 G 2 NAG A 1121 NAG # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 6 A CYS 6 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 112 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 B SG CYS 26 B CYS 231 1_555 B SG CYS 69 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 B SG CYS 62 B CYS 267 1_555 B SG CYS 102 B CYS 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 92 B CYS 297 1_555 B SG CYS 108 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf6 D SG CYS 6 D CYS 6 1_555 D SG CYS 94 D CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 D SG CYS 30 D CYS 30 1_555 D SG CYS 112 D CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf8 E SG CYS 26 E CYS 231 1_555 E SG CYS 69 E CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf9 E SG CYS 62 E CYS 267 1_555 E SG CYS 102 E CYS 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 E SG CYS 92 E CYS 297 1_555 E SG CYS 108 E CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 5 A ASN 5 1_555 H C1 NAG . A NAG 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A ND2 ASN 95 A ASN 95 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 B SG CYS 29 B CYS 234 1_555 J C11 GDI . B GDI 1369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? covale ? covale4 B ND2 ASN 47 B ASN 252 1_555 I C1 NAG . B NAG 1368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale5 E SG CYS 29 E CYS 234 1_555 M C11 GDI . E GDI 1369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? covale ? covale6 E ND2 ASN 47 E ASN 252 1_555 L C1 NAG . E NAG 1368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _chem_comp.formula 'C22 H24 N4 O' _chem_comp.formula_weight 360.452 _chem_comp.id GDI _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]PIPERIDINE-2-CARBOXAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C3 GDI sing 83 n n N1 C4 GDI sing 84 n n C2 C3 GDI sing 85 n n C2 C6 GDI sing 86 n n C4 C5 GDI sing 87 n n C4 C7 GDI sing 88 n n C5 C6 GDI sing 89 n n C7 O8 GDI doub 90 n n C7 N9 GDI sing 91 n n N9 C10 GDI sing 92 n n C10 C11 GDI sing 93 n n C10 C12 GDI sing 94 n n C11 N27 GDI doub 95 n n C11 H11 GDI sing 96 n n C12 C13 GDI sing 97 n n C13 C14 GDI sing 98 n y C13 C18 GDI doub 99 n y C14 C15 GDI doub 100 n y C15 C16 GDI sing 101 n y C16 C17 GDI doub 102 n y C16 C19 GDI sing 103 n n C17 C18 GDI sing 104 n y C19 C20 GDI sing 105 n y C19 C21 GDI doub 106 n y C20 C22 GDI doub 107 n y C21 C23 GDI sing 108 n y C22 C24 GDI sing 109 n y C23 C24 GDI doub 110 n y C24 C25 GDI sing 111 n n C25 N26 GDI trip 112 n n N1 H1 GDI sing 113 n n C3 H31C GDI sing 114 n n C3 H32C GDI sing 115 n n C4 H4 GDI sing 116 n n C2 H21C GDI sing 117 n n C2 H22C GDI sing 118 n n C6 H61C GDI sing 119 n n C6 H62C GDI sing 120 n n C5 H51C GDI sing 121 n n C5 H52C GDI sing 122 n n N9 H9 GDI sing 123 n n C10 H10 GDI sing 124 n n C12 H121 GDI sing 125 n n C12 H122 GDI sing 126 n n N27 H27 GDI sing 127 n n C14 H14 GDI sing 128 n n C18 H18 GDI sing 129 n n C15 H15 GDI sing 130 n n C17 H17 GDI sing 131 n n C20 H20 GDI sing 132 n n C21 H21 GDI sing 133 n n C22 H22 GDI sing 134 n n C23 H23 GDI sing 135 n n # _atom_sites.entry_id 4CDD _atom_sites.fract_transf_matrix[1][1] 0.011864 _atom_sites.fract_transf_matrix[1][2] 0.006849 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013699 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004523 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code H 5 NAG A 1 1119 1119 NAG NAG . I 5 NAG B 1 1368 1368 NAG NAG . J 6 GDI B 1 1369 1369 GDI GDI . K 7 CL B 1 1370 1370 CL CL . L 5 NAG E 1 1368 1368 NAG NAG . M 6 GDI E 1 1369 1369 GDI GDI . N 7 CL E 1 1370 1370 CL CL . O 8 HOH A 1 2001 2001 HOH HOH . O 8 HOH A 2 2002 2002 HOH HOH . O 8 HOH A 3 2003 2003 HOH HOH . O 8 HOH A 4 2004 2004 HOH HOH . O 8 HOH A 5 2005 2005 HOH HOH . O 8 HOH A 6 2006 2006 HOH HOH . O 8 HOH A 7 2007 2007 HOH HOH . O 8 HOH A 8 2008 2008 HOH HOH . O 8 HOH A 9 2009 2009 HOH HOH . O 8 HOH A 10 2010 2010 HOH HOH . O 8 HOH A 11 2011 2011 HOH HOH . O 8 HOH A 12 2012 2012 HOH HOH . O 8 HOH A 13 2013 2013 HOH HOH . O 8 HOH A 14 2014 2014 HOH HOH . O 8 HOH A 15 2015 2015 HOH HOH . O 8 HOH A 16 2016 2016 HOH HOH . O 8 HOH A 17 2017 2017 HOH HOH . O 8 HOH A 18 2018 2018 HOH HOH . O 8 HOH A 19 2019 2019 HOH HOH . O 8 HOH A 20 2020 2020 HOH HOH . O 8 HOH A 21 2021 2021 HOH HOH . O 8 HOH A 22 2022 2022 HOH HOH . O 8 HOH A 23 2023 2023 HOH HOH . O 8 HOH A 24 2024 2024 HOH HOH . O 8 HOH A 25 2025 2025 HOH HOH . P 8 HOH B 1 2001 2001 HOH HOH . P 8 HOH B 2 2002 2002 HOH HOH . P 8 HOH B 3 2003 2003 HOH HOH . P 8 HOH B 4 2004 2004 HOH HOH . P 8 HOH B 5 2005 2005 HOH HOH . P 8 HOH B 6 2006 2006 HOH HOH . P 8 HOH B 7 2007 2007 HOH HOH . P 8 HOH B 8 2008 2008 HOH HOH . P 8 HOH B 9 2009 2009 HOH HOH . P 8 HOH B 10 2010 2010 HOH HOH . P 8 HOH B 11 2011 2011 HOH HOH . P 8 HOH B 12 2012 2012 HOH HOH . P 8 HOH B 13 2013 2013 HOH HOH . P 8 HOH B 14 2014 2014 HOH HOH . P 8 HOH B 15 2015 2015 HOH HOH . P 8 HOH B 16 2016 2016 HOH HOH . P 8 HOH B 17 2017 2017 HOH HOH . P 8 HOH B 18 2018 2018 HOH HOH . P 8 HOH B 19 2019 2019 HOH HOH . P 8 HOH B 20 2020 2020 HOH HOH . P 8 HOH B 21 2021 2021 HOH HOH . P 8 HOH B 22 2022 2022 HOH HOH . P 8 HOH B 23 2023 2023 HOH HOH . P 8 HOH B 24 2024 2024 HOH HOH . P 8 HOH B 25 2025 2025 HOH HOH . P 8 HOH B 26 2026 2026 HOH HOH . P 8 HOH B 27 2027 2027 HOH HOH . P 8 HOH B 28 2028 2028 HOH HOH . P 8 HOH B 29 2029 2029 HOH HOH . P 8 HOH B 30 2030 2030 HOH HOH . P 8 HOH B 31 2031 2031 HOH HOH . Q 8 HOH C 1 2001 2001 HOH HOH . Q 8 HOH C 2 2002 2002 HOH HOH . Q 8 HOH C 3 2003 2003 HOH HOH . Q 8 HOH C 4 2004 2004 HOH HOH . Q 8 HOH C 5 2005 2005 HOH HOH . Q 8 HOH C 6 2006 2006 HOH HOH . R 8 HOH D 1 2001 2001 HOH HOH . R 8 HOH D 2 2002 2002 HOH HOH . R 8 HOH D 3 2003 2003 HOH HOH . R 8 HOH D 4 2004 2004 HOH HOH . R 8 HOH D 5 2005 2005 HOH HOH . R 8 HOH D 6 2006 2006 HOH HOH . R 8 HOH D 7 2007 2007 HOH HOH . R 8 HOH D 8 2008 2008 HOH HOH . R 8 HOH D 9 2009 2009 HOH HOH . R 8 HOH D 10 2010 2010 HOH HOH . R 8 HOH D 11 2011 2011 HOH HOH . R 8 HOH D 12 2012 2012 HOH HOH . R 8 HOH D 13 2013 2013 HOH HOH . R 8 HOH D 14 2014 2014 HOH HOH . R 8 HOH D 15 2015 2015 HOH HOH . R 8 HOH D 16 2016 2016 HOH HOH . R 8 HOH D 17 2017 2017 HOH HOH . R 8 HOH D 18 2018 2018 HOH HOH . S 8 HOH E 1 2001 2001 HOH HOH . S 8 HOH E 2 2002 2002 HOH HOH . S 8 HOH E 3 2003 2003 HOH HOH . S 8 HOH E 4 2004 2004 HOH HOH . S 8 HOH E 5 2005 2005 HOH HOH . S 8 HOH E 6 2006 2006 HOH HOH . S 8 HOH E 7 2007 2007 HOH HOH . S 8 HOH E 8 2008 2008 HOH HOH . S 8 HOH E 9 2009 2009 HOH HOH . S 8 HOH E 10 2010 2010 HOH HOH . S 8 HOH E 11 2011 2011 HOH HOH . S 8 HOH E 12 2012 2012 HOH HOH . S 8 HOH E 13 2013 2013 HOH HOH . S 8 HOH E 14 2014 2014 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 GDI . . . M 6 6.183 -11.852 6.301 1 54.34 ? N1 GDI 1369 E 1 HETATM 2 C C2 GDI . . . M 6 5.011 -12.47 8.406 1 62.91 ? C2 GDI 1369 E 1 HETATM 3 C C3 GDI . . . M 6 5.627 -12.961 7.087 1 53.39 ? C3 GDI 1369 E 1 HETATM 4 C C4 GDI . . . M 6 5.164 -10.833 6.013 1 56.29 ? C4 GDI 1369 E 1 HETATM 5 C C5 GDI . . . M 6 4.684 -10.224 7.333 1 58.48 ? C5 GDI 1369 E 1 HETATM 6 C C6 GDI . . . M 6 4.027 -11.317 8.187 1 60.42 ? C6 GDI 1369 E 1 HETATM 7 C C7 GDI . . . M 6 5.742 -9.754 5.121 1 65.02 ? C7 GDI 1369 E 1 HETATM 8 O O8 GDI . . . M 6 6.919 -9.807 4.802 1 56.8 ? O8 GDI 1369 E 1 HETATM 9 N N9 GDI . . . M 6 4.932 -8.747 4.697 1 65.83 ? N9 GDI 1369 E 1 HETATM 10 C C10 GDI . . . M 6 5.372 -7.636 3.833 1 65.36 ? C10 GDI 1369 E 1 HETATM 11 C C11 GDI . . . M 6 5.12 -6.406 4.583 1 60.93 ? C11 GDI 1369 E 1 HETATM 12 C C12 GDI . . . M 6 4.564 -7.658 2.52 1 65.16 ? C12 GDI 1369 E 1 HETATM 13 C C13 GDI . . . M 6 4.88 -8.906 1.727 1 61.41 ? C13 GDI 1369 E 1 HETATM 14 C C14 GDI . . . M 6 4.038 -10.018 1.807 1 61.78 ? C14 GDI 1369 E 1 HETATM 15 C C15 GDI . . . M 6 4.312 -11.171 1.089 1 57.48 ? C15 GDI 1369 E 1 HETATM 16 C C16 GDI . . . M 6 5.452 -11.22 0.283 1 57.79 ? C16 GDI 1369 E 1 HETATM 17 C C17 GDI . . . M 6 6.292 -10.095 0.199 1 60.75 ? C17 GDI 1369 E 1 HETATM 18 C C18 GDI . . . M 6 6.009 -8.944 0.922 1 59.49 ? C18 GDI 1369 E 1 HETATM 19 C C19 GDI . . . M 6 5.795 -12.424 -0.516 1 58.09 ? C19 GDI 1369 E 1 HETATM 20 C C20 GDI . . . M 6 7.118 -12.546 -0.963 1 60.33 ? C20 GDI 1369 E 1 HETATM 21 C C21 GDI . . . M 6 4.847 -13.414 -0.835 1 65.45 ? C21 GDI 1369 E 1 HETATM 22 C C22 GDI . . . M 6 7.504 -13.639 -1.705 1 59.71 ? C22 GDI 1369 E 1 HETATM 23 C C23 GDI . . . M 6 5.22 -14.516 -1.596 1 62.45 ? C23 GDI 1369 E 1 HETATM 24 C C24 GDI . . . M 6 6.552 -14.623 -2.031 1 67.68 ? C24 GDI 1369 E 1 HETATM 25 C C25 GDI . . . M 6 6.997 -15.731 -2.821 1 74.94 ? C25 GDI 1369 E 1 HETATM 26 N N26 GDI . . . M 6 7.378 -16.6 -3.445 1 65.23 ? N26 GDI 1369 E 1 HETATM 27 N N27 GDI . . . M 6 4.978 -5.288 4.027 1 55.25 ? N27 GDI 1369 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #