data_5L1F
#
_model_server_result.job_id            yvNjauskJJhbzmgLVzMSuQ 
_model_server_result.datetime_utc      '2024-11-08 18:00:48' 
_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          5l1f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":902}' 
#
_entry.id    5L1F 
#
_exptl.entry_id    5L1F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              349.385 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile" 
_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            5L1F 
_cell.length_a            91.74 
_cell.length_b            109.345 
_cell.length_c            594.835 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5L1F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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 54 A CYS 63 1_555 A SG CYS 306 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 690 A CYS 718 1_555 A SG CYS 745 A CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 B SG CYS 54 B CYS 63 1_555 B SG CYS 306 B CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 B SG CYS 690 B CYS 718 1_555 B SG CYS 745 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 C SG CYS 54 C CYS 63 1_555 C SG CYS 306 C CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 C SG CYS 690 C CYS 718 1_555 C SG CYS 745 C CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 D SG CYS 54 D CYS 63 1_555 D SG CYS 306 D CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
covale ? covale1 A NZ LYS 337 A LYS 346 1_555 E O7 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? 
covale ? covale2 A ND2 ASN 346 A ASN 355 1_555 E C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale3 B ND2 ASN 346 B ASN 355 1_555 G C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale4 C NZ LYS 337 C LYS 346 1_555 I O7 NAG . C NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
covale ? covale5 C ND2 ASN 346 C ASN 355 1_555 I C1 NAG . C NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale6 D ND2 ASN 346 D ASN 355 1_555 K C1 NAG . D NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
#
_chem_comp.formula           'C23 H15 N3 O' 
_chem_comp.formula_weight    349.385 
_chem_comp.id                6ZP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile" 
_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
C24 C25 6ZP doub 1 n y 
C24 C23 6ZP sing 2 n y 
C25 C26 6ZP sing 3 n y 
C23 C22 6ZP doub 4 n y 
N01 C02 6ZP trip 5 n n 
C26 C27 6ZP doub 6 n y 
C02 C03 6ZP sing 7 n n 
C22 C27 6ZP sing 8 n y 
C22 N21 6ZP sing 9 n n 
O11 C10 6ZP doub 10 n n 
C03 C04 6ZP doub 11 n y 
C03 C08 6ZP sing 12 n y 
C04 C05 6ZP sing 13 n y 
C10 N21 6ZP sing 14 n n 
C10 C09 6ZP sing 15 n n 
N21 C20 6ZP sing 16 n n 
C08 C09 6ZP sing 17 n n 
C08 C07 6ZP doub 18 n y 
C05 C06 6ZP doub 19 n y 
C09 C12 6ZP doub 20 n n 
C20 C13 6ZP doub 21 n n 
C13 C12 6ZP sing 22 n n 
C13 C14 6ZP sing 23 n n 
C07 C06 6ZP sing 24 n y 
C19 C14 6ZP doub 25 n y 
C19 C18 6ZP sing 26 n y 
C14 N15 6ZP sing 27 n y 
C18 C17 6ZP doub 28 n y 
N15 C16 6ZP doub 29 n y 
C17 C16 6ZP sing 30 n y 
C04 H1 6ZP sing 31 n n 
C05 H2 6ZP sing 32 n n 
C06 H3 6ZP sing 33 n n 
C07 H4 6ZP sing 34 n n 
C12 H5 6ZP sing 35 n n 
C16 H6 6ZP sing 36 n n 
C17 H7 6ZP sing 37 n n 
C18 H8 6ZP sing 38 n n 
C19 H9 6ZP sing 39 n n 
C20 H10 6ZP sing 40 n n 
C23 H11 6ZP sing 41 n n 
C24 H12 6ZP sing 42 n n 
C25 H13 6ZP sing 43 n n 
C26 H14 6ZP sing 44 n n 
C27 H15 6ZP sing 45 n n 
#
_atom_sites.entry_id                     5L1F 
_atom_sites.fract_transf_matrix[1][1]    0.0109 
_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]    0.009145 
_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]    0.001681 
_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
E 2 NAG A 1 901 834 NAG NAG . 
F 3 6ZP A 1 902 903 6ZP PMP . 
G 2 NAG B 1 901 834 NAG NAG . 
H 3 6ZP B 1 902 903 6ZP PMP . 
I 2 NAG C 1 901 834 NAG NAG . 
J 3 6ZP C 1 902 903 6ZP PMP . 
K 2 NAG D 1 901 834 NAG NAG . 
L 3 6ZP D 1 902 903 6ZP PMP . 
#
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 N01 6ZP . . . H 3 -39.429 -19.704 -49.978 1 135.49 ? N01 6ZP 902 B 1 
HETATM 2 C C02 6ZP . . . H 3 -40.163 -18.854 -49.835 1 202.4 ? C02 6ZP 902 B 1 
HETATM 3 C C03 6ZP . . . H 3 -41.154 -17.706 -49.644 1 215.37 ? C03 6ZP 902 B 1 
HETATM 4 C C04 6ZP . . . H 3 -42.011 -17.355 -50.675 1 215.37 ? C04 6ZP 902 B 1 
HETATM 5 C C05 6ZP . . . H 3 -42.91 -16.315 -50.505 1 215.37 ? C05 6ZP 902 B 1 
HETATM 6 C C06 6ZP . . . H 3 -42.954 -15.626 -49.303 1 215.37 ? C06 6ZP 902 B 1 
HETATM 7 C C07 6ZP . . . H 3 -42.097 -15.977 -48.272 1 215.37 ? C07 6ZP 902 B 1 
HETATM 8 C C08 6ZP . . . H 3 -41.197 -17.017 -48.441 1 215.37 ? C08 6ZP 902 B 1 
HETATM 9 C C09 6ZP . . . H 3 -40.34 -17.366 -47.405 1 212.61 ? C09 6ZP 902 B 1 
HETATM 10 C C10 6ZP . . . H 3 -38.952 -17.199 -47.512 1 209.18 ? C10 6ZP 902 B 1 
HETATM 11 O O11 6ZP . . . H 3 -38.512 -16.745 -48.525 1 215.37 ? O11 6ZP 902 B 1 
HETATM 12 C C12 6ZP . . . H 3 -40.861 -17.892 -46.234 1 210.24 ? C12 6ZP 902 B 1 
HETATM 13 C C13 6ZP . . . H 3 -40.006 -18.234 -45.215 1 215.37 ? C13 6ZP 902 B 1 
HETATM 14 C C14 6ZP . . . H 3 -40.51 -18.762 -44.036 1 215.37 ? C14 6ZP 902 B 1 
HETATM 15 N N15 6ZP . . . H 3 -41.428 -18.091 -43.362 1 215.37 ? N15 6ZP 902 B 1 
HETATM 16 C C16 6ZP . . . H 3 -41.938 -18.554 -42.234 1 215.37 ? C16 6ZP 902 B 1 
HETATM 17 C C17 6ZP . . . H 3 -41.514 -19.771 -41.725 1 173.26 ? C17 6ZP 902 B 1 
HETATM 18 C C18 6ZP . . . H 3 -40.553 -20.504 -42.402 1 156.73 ? C18 6ZP 902 B 1 
HETATM 19 C C19 6ZP . . . H 3 -40.043 -19.986 -43.582 1 200.16 ? C19 6ZP 902 B 1 
HETATM 20 C C20 6ZP . . . H 3 -38.651 -18.053 -45.363 1 215.37 ? C20 6ZP 902 B 1 
HETATM 21 N N21 6ZP . . . H 3 -38.156 -17.551 -46.482 1 214.1 ? N21 6ZP 902 B 1 
HETATM 22 C C22 6ZP . . . H 3 -36.834 -17.414 -46.53 1 215.37 ? C22 6ZP 902 B 1 
HETATM 23 C C23 6ZP . . . H 3 -36.106 -18.06 -47.516 1 215.37 ? C23 6ZP 902 B 1 
HETATM 24 C C24 6ZP . . . H 3 -34.728 -17.917 -47.566 1 215.37 ? C24 6ZP 902 B 1 
HETATM 25 C C25 6ZP . . . H 3 -34.079 -17.128 -46.631 1 203.94 ? C25 6ZP 902 B 1 
HETATM 26 C C26 6ZP . . . H 3 -34.806 -16.482 -45.646 1 199.3 ? C26 6ZP 902 B 1 
HETATM 27 C C27 6ZP . . . H 3 -36.184 -16.624 -45.595 1 211.59 ? C27 6ZP 902 B 1 
#
_model_server_stats.io_time_ms              100 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#