data_5VRP # _model_server_result.job_id zI-9ifoCj4lFJrKa-q-opg _model_server_result.datetime_utc '2024-11-16 23:50:22' _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 5vrp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 5VRP # _exptl.entry_id 5VRP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 529.643 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "methyl [(4S)-4-{(3R)-1-[(3S)-4-amino-3-hydroxybutanoyl]piperidin-3-yl}-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxybutyl]carbamate" _entity.pdbx_number_of_molecules 4 _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 90 _cell.entry_id 5VRP _cell.length_a 54.334 _cell.length_b 99.933 _cell.length_c 146.529 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VRP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I,J 2 1 A,B,C,D,E,F,G,H,I,J 3 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 ? 4 E N N ? 4 F N N ? 4 H N N ? 4 I 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 48 A CYS 117 1_555 A SG CYS 55 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 214 A CYS 283 1_555 A SG CYS 218 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 256 A CYS 325 1_555 A SG CYS 293 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 48 B CYS 117 1_555 B SG CYS 55 B CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 214 B CYS 283 1_555 B SG CYS 218 B CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 256 B CYS 325 1_555 B SG CYS 293 B CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 B ND2 ASN 72 B ASN 141 1_555 G C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _chem_comp.formula 'C29 H40 F N3 O5' _chem_comp.formula_weight 529.643 _chem_comp.id 9JD _chem_comp.mon_nstd_flag . _chem_comp.name "methyl [(4S)-4-{(3R)-1-[(3S)-4-amino-3-hydroxybutanoyl]piperidin-3-yl}-4-(3'-ethyl-6-fluoro[1,1'-biphenyl]-2-yl)-4-hydroxybutyl]carbamate" _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 N40 C39 9JD sing 1 n n C39 C36 9JD sing 2 n n C01 C02 9JD sing 3 n n C36 O38 9JD sing 4 n n C36 C35 9JD sing 5 n n C02 C03 9JD sing 6 n n C04 C03 9JD doub 7 n y C04 C05 9JD sing 8 n y C35 C33 9JD sing 9 n n C03 C08 9JD sing 10 n y O34 C33 9JD doub 11 n n C05 C06 9JD doub 12 n y C33 N31 9JD sing 13 n n C08 C07 9JD doub 14 n y C06 C07 9JD sing 15 n y N31 C30 9JD sing 16 n n N31 C32 9JD sing 17 n n N21 C20 9JD sing 18 n n N21 C22 9JD sing 19 n n C07 C09 9JD sing 20 n n C20 C19 9JD sing 21 n n O24 C22 9JD sing 22 n n O24 C25 9JD sing 23 n n C22 O23 9JD doub 24 n n C30 C29 9JD sing 25 n n C32 C26 9JD sing 26 n n C18 C19 9JD sing 27 n n C18 C16 9JD sing 28 n n C26 C16 9JD sing 29 n n C26 C28 9JD sing 30 n n C29 C28 9JD sing 31 n n F11 C10 9JD sing 32 n n C09 C10 9JD doub 33 n y C09 C15 9JD sing 34 n y C16 C15 9JD sing 35 n n C16 O17 9JD sing 36 n n C10 C12 9JD sing 37 n y C15 C14 9JD doub 38 n y C12 C13 9JD doub 39 n y C14 C13 9JD sing 40 n y C12 H1 9JD sing 41 n n C13 H2 9JD sing 42 n n C14 H3 9JD sing 43 n n C18 H4 9JD sing 44 n n C18 H5 9JD sing 45 n n C19 H6 9JD sing 46 n n C19 H7 9JD sing 47 n n N21 H8 9JD sing 48 n n C01 H9 9JD sing 49 n n C01 H10 9JD sing 50 n n C01 H11 9JD sing 51 n n C02 H12 9JD sing 52 n n C02 H13 9JD sing 53 n n C04 H14 9JD sing 54 n n C05 H15 9JD sing 55 n n C06 H16 9JD sing 56 n n C08 H17 9JD sing 57 n n O17 H18 9JD sing 58 n n C20 H19 9JD sing 59 n n C20 H20 9JD sing 60 n n C25 H21 9JD sing 61 n n C25 H22 9JD sing 62 n n C25 H23 9JD sing 63 n n C26 H24 9JD sing 64 n n C28 H25 9JD sing 65 n n C28 H26 9JD sing 66 n n C29 H27 9JD sing 67 n n C29 H28 9JD sing 68 n n C30 H29 9JD sing 69 n n C30 H30 9JD sing 70 n n C32 H31 9JD sing 71 n n C32 H32 9JD sing 72 n n C35 H33 9JD sing 73 n n C35 H34 9JD sing 74 n n C36 H35 9JD sing 75 n n O38 H36 9JD sing 76 n n C39 H37 9JD sing 77 n n C39 H38 9JD sing 78 n n N40 H39 9JD sing 79 n n N40 H40 9JD sing 80 n n # _atom_sites.entry_id 5VRP _atom_sites.fract_transf_matrix[1][1] 0.018405 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010007 _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] 0.006825 _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 C 2 NAG A 1 501 459 NAG NAG . D 3 SO4 A 1 502 2 SO4 SO4 . E 4 9JD A 1 503 1 9JD 604 . F 4 9JD A 1 504 4 9JD 604 . G 2 NAG B 1 501 459 NAG NAG . H 4 9JD B 1 502 2 9JD 604 . I 4 9JD B 1 503 3 9JD 604 . J 5 HOH B 1 601 2 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 C10 9JD . . . F 4 24.745 36.2 19.095 0.66 33.76 ? C10 9JD 504 A 1 HETATM 2 C C12 9JD . . . F 4 23.673 36.392 18.268 0.66 33.76 ? C12 9JD 504 A 1 HETATM 3 C C13 9JD . . . F 4 23.384 37.684 17.868 0.66 33.76 ? C13 9JD 504 A 1 HETATM 4 C C14 9JD . . . F 4 24.166 38.746 18.297 0.66 33.76 ? C14 9JD 504 A 1 HETATM 5 C C15 9JD . . . F 4 25.254 38.542 19.141 0.66 33.76 ? C15 9JD 504 A 1 HETATM 6 C C16 9JD . . . F 4 26.11 39.744 19.601 0.66 33.76 ? C16 9JD 504 A 1 HETATM 7 C C18 9JD . . . F 4 27.591 39.608 19.199 0.66 33.76 ? C18 9JD 504 A 1 HETATM 8 C C19 9JD . . . F 4 27.843 39.045 17.798 0.66 33.76 ? C19 9JD 504 A 1 HETATM 9 N N21 9JD . . . F 4 29.435 39.506 15.968 0.66 33.76 ? N21 9JD 504 A 1 HETATM 10 O O23 9JD . . . F 4 31.605 38.913 15.777 0.66 33.76 ? O23 9JD 504 A 1 HETATM 11 O O24 9JD . . . F 4 30.49 39.832 14.053 0.66 33.76 ? O24 9JD 504 A 1 HETATM 12 C C01 9JD . . . F 4 27.152 38.474 24.534 0.66 33.76 ? C01 9JD 504 A 1 HETATM 13 C C02 9JD . . . F 4 27.506 37.045 24.178 0.66 33.76 ? C02 9JD 504 A 1 HETATM 14 C C03 9JD . . . F 4 27.654 36.826 22.684 0.66 33.76 ? C03 9JD 504 A 1 HETATM 15 C C04 9JD . . . F 4 28.834 36.331 22.144 0.66 33.76 ? C04 9JD 504 A 1 HETATM 16 C C05 9JD . . . F 4 28.955 36.127 20.781 0.66 33.76 ? C05 9JD 504 A 1 HETATM 17 C C06 9JD . . . F 4 27.898 36.412 19.938 0.66 33.76 ? C06 9JD 504 A 1 HETATM 18 C C07 9JD . . . F 4 26.702 36.905 20.451 0.66 33.76 ? C07 9JD 504 A 1 HETATM 19 C C08 9JD . . . F 4 26.598 37.1 21.825 0.66 33.76 ? C08 9JD 504 A 1 HETATM 20 C C09 9JD . . . F 4 25.558 37.225 19.552 0.66 33.76 ? C09 9JD 504 A 1 HETATM 21 F F11 9JD . . . F 4 25.036 34.942 19.493 0.66 33.76 ? F11 9JD 504 A 1 HETATM 22 O O17 9JD . . . F 4 25.614 40.923 18.957 0.66 33.76 ? O17 9JD 504 A 1 HETATM 23 C C20 9JD . . . F 4 29.295 39.079 17.362 0.66 33.76 ? C20 9JD 504 A 1 HETATM 24 C C22 9JD . . . F 4 30.593 39.38 15.308 0.66 33.76 ? C22 9JD 504 A 1 HETATM 25 C C25 9JD . . . F 4 31.688 39.702 13.251 0.66 33.76 ? C25 9JD 504 A 1 HETATM 26 C C26 9JD . . . F 4 25.742 40.164 21.105 0.66 33.76 ? C26 9JD 504 A 1 HETATM 27 C C28 9JD . . . F 4 24.235 40.367 21.363 0.66 33.76 ? C28 9JD 504 A 1 HETATM 28 C C29 9JD . . . F 4 23.949 40.943 22.742 0.66 33.76 ? C29 9JD 504 A 1 HETATM 29 C C30 9JD . . . F 4 24.762 42.189 22.976 0.66 33.76 ? C30 9JD 504 A 1 HETATM 30 N N31 9JD . . . F 4 26.196 41.898 22.805 0.66 33.76 ? N31 9JD 504 A 1 HETATM 31 C C32 9JD . . . F 4 26.494 41.442 21.445 0.66 33.76 ? C32 9JD 504 A 1 HETATM 32 C C33 9JD . . . F 4 27.16 42.014 23.749 0.66 33.76 ? C33 9JD 504 A 1 HETATM 33 O O34 9JD . . . F 4 28.325 41.748 23.503 0.66 33.76 ? O34 9JD 504 A 1 HETATM 34 C C35 9JD . . . F 4 26.767 42.493 25.132 0.66 33.76 ? C35 9JD 504 A 1 HETATM 35 C C36 9JD . . . F 4 27.823 42.145 26.179 0.66 33.76 ? C36 9JD 504 A 1 HETATM 36 O O38 9JD . . . F 4 27.251 41.226 27.113 0.66 33.76 ? O38 9JD 504 A 1 HETATM 37 C C39 9JD . . . F 4 28.204 43.39 27.034 0.66 33.76 ? C39 9JD 504 A 1 HETATM 38 N N40 9JD . . . F 4 29.104 43.124 28.156 0.66 33.76 ? N40 9JD 504 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 38 #