data_4CDF # _model_server_result.job_id ArYGHcyFvaY5s3K9f6YLBg _model_server_result.datetime_utc '2025-03-04 15:33:56' _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 4cdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":1369}' # _entry.id 4CDF # _exptl.entry_id 4CDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.452 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-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 4CDF _cell.length_a 84.85 _cell.length_b 84.85 _cell.length_c 222.452 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CDF _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 A,B,C,G,H,I,J,O,P,Q 1 1 D,E,F,K,L,M,N,R,S,T 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 ? 5 I N N ? 5 M N N # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 112 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 B SG CYS 27 B CYS 231 1_555 B SG CYS 70 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf4 B SG CYS 63 B CYS 267 1_555 B SG CYS 103 B CYS 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 93 B CYS 297 1_555 B SG CYS 109 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf6 D SG CYS 6 D CYS 6 1_555 D SG CYS 94 D CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 D SG CYS 30 D CYS 30 1_555 D SG CYS 112 D CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf8 E SG CYS 27 E CYS 231 1_555 E SG CYS 70 E CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf9 E SG CYS 63 E CYS 267 1_555 E SG CYS 103 E CYS 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 E SG CYS 93 E CYS 297 1_555 E SG CYS 109 E CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 95 A ASN 95 1_555 G C1 NAG . A NAG 1121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 B SG CYS 30 B CYS 234 1_555 I C9 W2C . B W2C 1369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? covale ? covale3 B ND2 ASN 48 B ASN 252 1_555 H C1 NAG . B NAG 1368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale4 D ND2 ASN 95 D ASN 95 1_555 K C1 NAG . D NAG 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 E SG CYS 30 E CYS 234 1_555 M C9 W2C . E W2C 1369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? covale ? covale6 E ND2 ASN 48 E ASN 252 1_555 L C1 NAG . E NAG 1368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _chem_comp.formula 'C22 H24 N4 O2' _chem_comp.formula_weight 376.452 _chem_comp.id W2C _chem_comp.mon_nstd_flag . _chem_comp.name (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-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 C27 C24 W2C sing 406 n n C27 N28 W2C trip 407 n n C9 C8 W2C sing 408 n n C9 N10 W2C doub 409 n n C9 H9 W2C sing 410 n n C23 C22 W2C doub 411 n y C23 C24 W2C sing 412 n y C25 C26 W2C sing 413 n y C25 C24 W2C doub 414 n y C22 C21 W2C sing 415 n y C26 C21 W2C doub 416 n y C2 C1 W2C sing 417 n y C2 C3 W2C doub 418 n y C4 C5 W2C doub 419 n y C4 C3 W2C sing 420 n y C1 C6 W2C doub 421 n y C5 C6 W2C sing 422 n y C21 C3 W2C sing 423 n n C6 C7 W2C sing 424 n n C12 C14 W2C sing 425 n n C12 N11 W2C sing 426 n n C12 O13 W2C doub 427 n n C17 C18 W2C sing 428 n n C17 C16 W2C sing 429 n n C15 C14 W2C sing 430 n n C15 C16 W2C sing 431 n n C18 N19 W2C sing 432 n n C14 N19 W2C sing 433 n n C16 O20 W2C sing 434 n n C7 C8 W2C sing 435 n n C8 N11 W2C sing 436 n n C8 H8 W2C sing 437 n n N10 H10 W2C sing 438 n n C23 H23 W2C sing 439 n n C22 H22 W2C sing 440 n n C25 H25 W2C sing 441 n n C26 H26 W2C sing 442 n n C2 H2 W2C sing 443 n n C1 H1 W2C sing 444 n n C4 H4 W2C sing 445 n n C5 H5 W2C sing 446 n n C7 H71C W2C sing 447 n n C7 H72C W2C sing 448 n n C14 H14 W2C sing 449 n n N11 H11 W2C sing 450 n n C17 H171 W2C sing 451 n n C17 H172 W2C sing 452 n n C18 H181 W2C sing 453 n n C18 H182 W2C sing 454 n n C16 H16 W2C sing 455 n n C15 H151 W2C sing 456 n n C15 H152 W2C sing 457 n n N19 H19 W2C sing 458 n n O20 H20 W2C sing 459 n n # _atom_sites.entry_id 4CDF _atom_sites.fract_transf_matrix[1][1] 0.011786 _atom_sites.fract_transf_matrix[1][2] 0.006804 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013609 _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] 0.004495 _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 G 4 NAG A 1 1121 1121 NAG NAG . H 4 NAG B 1 1368 1368 NAG NAG . I 5 W2C B 1 1369 1369 W2C W2C . J 6 CL B 1 1370 1370 CL CL . K 4 NAG D 1 1119 1119 NAG NAG . L 4 NAG E 1 1368 1368 NAG NAG . M 5 W2C E 1 1369 1369 W2C W2C . N 6 CL E 1 1370 1370 CL CL . O 7 HOH A 1 2001 2001 HOH HOH . O 7 HOH A 2 2002 2002 HOH HOH . O 7 HOH A 3 2003 2003 HOH HOH . O 7 HOH A 4 2004 2004 HOH HOH . O 7 HOH A 5 2005 2005 HOH HOH . O 7 HOH A 6 2006 2006 HOH HOH . O 7 HOH A 7 2007 2007 HOH HOH . O 7 HOH A 8 2008 2008 HOH HOH . O 7 HOH A 9 2009 2009 HOH HOH . O 7 HOH A 10 2010 2010 HOH HOH . O 7 HOH A 11 2011 2011 HOH HOH . O 7 HOH A 12 2012 2012 HOH HOH . O 7 HOH A 13 2013 2013 HOH HOH . O 7 HOH A 14 2014 2014 HOH HOH . O 7 HOH A 15 2015 2015 HOH HOH . O 7 HOH A 16 2016 2016 HOH HOH . O 7 HOH A 17 2017 2017 HOH HOH . O 7 HOH A 18 2018 2018 HOH HOH . O 7 HOH A 19 2019 2019 HOH HOH . O 7 HOH A 20 2020 2020 HOH HOH . O 7 HOH A 21 2021 2021 HOH HOH . O 7 HOH A 22 2022 2022 HOH HOH . O 7 HOH A 23 2023 2023 HOH HOH . O 7 HOH A 24 2024 2024 HOH HOH . O 7 HOH A 25 2025 2025 HOH HOH . O 7 HOH A 26 2026 2026 HOH HOH . O 7 HOH A 27 2027 2027 HOH HOH . O 7 HOH A 28 2028 2028 HOH HOH . O 7 HOH A 29 2029 2029 HOH HOH . O 7 HOH A 30 2030 2030 HOH HOH . O 7 HOH A 31 2031 2031 HOH HOH . O 7 HOH A 32 2032 2032 HOH HOH . O 7 HOH A 33 2033 2033 HOH HOH . P 7 HOH B 1 2001 2001 HOH HOH . P 7 HOH B 2 2002 2002 HOH HOH . P 7 HOH B 3 2003 2003 HOH HOH . P 7 HOH B 4 2004 2004 HOH HOH . P 7 HOH B 5 2005 2005 HOH HOH . P 7 HOH B 6 2006 2006 HOH HOH . P 7 HOH B 7 2007 2007 HOH HOH . P 7 HOH B 8 2008 2008 HOH HOH . P 7 HOH B 9 2009 2009 HOH HOH . P 7 HOH B 10 2010 2010 HOH HOH . P 7 HOH B 11 2011 2011 HOH HOH . P 7 HOH B 12 2012 2012 HOH HOH . P 7 HOH B 13 2013 2013 HOH HOH . P 7 HOH B 14 2014 2014 HOH HOH . P 7 HOH B 15 2015 2015 HOH HOH . P 7 HOH B 16 2016 2016 HOH HOH . P 7 HOH B 17 2017 2017 HOH HOH . P 7 HOH B 18 2018 2018 HOH HOH . P 7 HOH B 19 2019 2019 HOH HOH . P 7 HOH B 20 2020 2020 HOH HOH . P 7 HOH B 21 2021 2021 HOH HOH . P 7 HOH B 22 2022 2022 HOH HOH . P 7 HOH B 23 2023 2023 HOH HOH . P 7 HOH B 24 2024 2024 HOH HOH . P 7 HOH B 25 2025 2025 HOH HOH . P 7 HOH B 26 2026 2026 HOH HOH . P 7 HOH B 27 2027 2027 HOH HOH . P 7 HOH B 28 2028 2028 HOH HOH . P 7 HOH B 29 2029 2029 HOH HOH . Q 7 HOH C 1 2001 2001 HOH HOH . Q 7 HOH C 2 2002 2002 HOH HOH . Q 7 HOH C 3 2003 2003 HOH HOH . Q 7 HOH C 4 2004 2004 HOH HOH . Q 7 HOH C 5 2005 2005 HOH HOH . Q 7 HOH C 6 2006 2006 HOH HOH . Q 7 HOH C 7 2007 2007 HOH HOH . Q 7 HOH C 8 2008 2008 HOH HOH . R 7 HOH D 1 2001 2001 HOH HOH . R 7 HOH D 2 2002 2002 HOH HOH . R 7 HOH D 3 2003 2003 HOH HOH . R 7 HOH D 4 2004 2004 HOH HOH . R 7 HOH D 5 2005 2005 HOH HOH . R 7 HOH D 6 2006 2006 HOH HOH . R 7 HOH D 7 2007 2007 HOH HOH . R 7 HOH D 8 2008 2008 HOH HOH . R 7 HOH D 9 2009 2009 HOH HOH . R 7 HOH D 10 2010 2010 HOH HOH . R 7 HOH D 11 2011 2011 HOH HOH . R 7 HOH D 12 2012 2012 HOH HOH . R 7 HOH D 13 2013 2013 HOH HOH . R 7 HOH D 14 2014 2014 HOH HOH . R 7 HOH D 15 2015 2015 HOH HOH . R 7 HOH D 16 2016 2016 HOH HOH . R 7 HOH D 17 2017 2017 HOH HOH . R 7 HOH D 18 2018 2018 HOH HOH . R 7 HOH D 19 2019 2019 HOH HOH . R 7 HOH D 20 2020 2020 HOH HOH . R 7 HOH D 21 2021 2021 HOH HOH . R 7 HOH D 22 2022 2022 HOH HOH . S 7 HOH E 1 2001 2001 HOH HOH . S 7 HOH E 2 2002 2002 HOH HOH . S 7 HOH E 3 2003 2003 HOH HOH . S 7 HOH E 4 2004 2004 HOH HOH . S 7 HOH E 5 2005 2005 HOH HOH . S 7 HOH E 6 2006 2006 HOH HOH . S 7 HOH E 7 2007 2007 HOH HOH . S 7 HOH E 8 2008 2008 HOH HOH . S 7 HOH E 9 2009 2009 HOH HOH . S 7 HOH E 10 2010 2010 HOH HOH . S 7 HOH E 11 2011 2011 HOH HOH . S 7 HOH E 12 2012 2012 HOH HOH . S 7 HOH E 13 2013 2013 HOH HOH . S 7 HOH E 14 2014 2014 HOH HOH . S 7 HOH E 15 2015 2015 HOH HOH . S 7 HOH E 16 2016 2016 HOH HOH . S 7 HOH E 17 2017 2017 HOH HOH . S 7 HOH E 18 2018 2018 HOH HOH . S 7 HOH E 19 2019 2019 HOH HOH . S 7 HOH E 20 2020 2020 HOH HOH . T 7 HOH F 1 2001 2001 HOH HOH . T 7 HOH F 2 2002 2002 HOH HOH . T 7 HOH F 3 2003 2003 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 C C27 W2C . . . M 5 25.189 75.373 34.291 1 54.43 ? C27 W2C 1369 E 1 HETATM 2 C C9 W2C . . . M 5 34.241 72.36 41.706 1 41.97 ? C9 W2C 1369 E 1 HETATM 3 C C23 W2C . . . M 5 27.227 76.282 35.386 1 53.42 ? C23 W2C 1369 E 1 HETATM 4 C C25 W2C . . . M 5 26.677 73.975 35.499 1 52.7 ? C25 W2C 1369 E 1 HETATM 5 C C22 W2C . . . M 5 28.363 76.04 36.136 1 55.53 ? C22 W2C 1369 E 1 HETATM 6 C C26 W2C . . . M 5 27.813 73.757 36.243 1 53.48 ? C26 W2C 1369 E 1 HETATM 7 C C2 W2C . . . M 5 30.455 75.385 38.24 1 44.01 ? C2 W2C 1369 E 1 HETATM 8 C C4 W2C . . . M 5 30.497 73.257 37.222 1 48.46 ? C4 W2C 1369 E 1 HETATM 9 C C1 W2C . . . M 5 31.584 75.043 38.963 1 46.83 ? C1 W2C 1369 E 1 HETATM 10 C C5 W2C . . . M 5 31.62 72.918 37.938 1 45.65 ? C5 W2C 1369 E 1 HETATM 11 C C24 W2C . . . M 5 26.38 75.242 35.067 1 55.85 ? C24 W2C 1369 E 1 HETATM 12 C C21 W2C . . . M 5 28.686 74.772 36.582 1 51.64 ? C21 W2C 1369 E 1 HETATM 13 C C3 W2C . . . M 5 29.888 74.492 37.358 1 48.25 ? C3 W2C 1369 E 1 HETATM 14 C C6 W2C . . . M 5 32.183 73.801 38.82 1 46.02 ? C6 W2C 1369 E 1 HETATM 15 C C12 W2C . . . M 5 31.047 73.175 42.241 1 47.43 ? C12 W2C 1369 E 1 HETATM 16 C C17 W2C . . . M 5 28.83 75.236 45.188 1 41.34 ? C17 W2C 1369 E 1 HETATM 17 C C15 W2C . . . M 5 31.041 74.547 44.193 1 46.76 ? C15 W2C 1369 E 1 HETATM 18 C C18 W2C . . . M 5 28.241 74.958 43.824 1 44.03 ? C18 W2C 1369 E 1 HETATM 19 C C14 W2C . . . M 5 30.301 74.292 42.894 1 44.94 ? C14 W2C 1369 E 1 HETATM 20 C C16 W2C . . . M 5 30.321 75.519 45.104 1 46.17 ? C16 W2C 1369 E 1 HETATM 21 C C7 W2C . . . M 5 33.396 73.377 39.596 1 45.63 ? C7 W2C 1369 E 1 HETATM 22 C C8 W2C . . . M 5 33.048 72.699 40.922 1 44.7 ? C8 W2C 1369 E 1 HETATM 23 N N28 W2C . . . M 5 24.193 75.447 33.692 1 48.35 ? N28 W2C 1369 E 1 HETATM 24 N N10 W2C . . . M 5 35.303 72.035 41.125 1 42.46 ? N10 W2C 1369 E 1 HETATM 25 N N19 W2C . . . M 5 28.945 73.863 43.189 1 40.85 ? N19 W2C 1369 E 1 HETATM 26 N N11 W2C . . . M 5 32.211 73.604 41.654 1 46.73 ? N11 W2C 1369 E 1 HETATM 27 O O13 W2C . . . M 5 30.63 72.023 42.288 1 44.87 ? O13 W2C 1369 E 1 HETATM 28 O O20 W2C . . . M 5 30.56 76.822 44.602 1 49.98 ? O20 W2C 1369 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #