data_7EFN
#
_model_server_result.job_id            Xr9d66h4E6U9EURfhdb73g 
_model_server_result.datetime_utc      '2024-10-19 12:35:45' 
_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          7efn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1104}' 
#
_entry.id    7EFN 
#
_exptl.entry_id    7EFN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              309.362 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol 
_entity.pdbx_number_of_molecules    1 
_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            7EFN 
_cell.length_a            105.94 
_cell.length_b            105.94 
_cell.length_c            372.01 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7EFN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,M 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 479 A CYS 527 1_555 A SG CYS 517 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf2 B SG CYS 102 B CYS 131 1_555 B SG CYS 123 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 B SG CYS 133 B CYS 162 1_555 B SG CYS 149 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf4 B SG CYS 172 B CYS 201 1_555 B SG CYS 233 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
covale ? covale1 A C SER 336 A SER 384 1_555 A N BFD 337 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C BFD 337 A BFD 385 1_555 A N LYS 338 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale3 B ND2 ASN 70 B ASN 99 1_555 I C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale4 B ND2 ASN 101 B ASN 130 1_555 J C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale5 B ND2 ASN 132 B ASN 161 1_555 K C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
metalc ? metalc1 A OD1 ASP 137 A ASP 185 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc2 A OD2 ASP 137 A ASP 185 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? 
metalc ? metalc3 A O ALA 291 A ALA 339 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? 
metalc ? metalc4 A O SER 360 A SER 408 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? 
metalc ? metalc5 A O GLN 370 A GLN 418 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? 
metalc ? metalc6 A O THR 371 A THR 419 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.2 ? 
metalc ? metalc7 A OD1 ASP 678 A ASP 726 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc8 A OD2 ASP 678 A ASP 726 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc9 A O LEU 686 A LEU 734 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? 
metalc ? metalc10 A O LYS 687 A LYS 735 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? 
metalc ? metalc11 A O ALA 689 A ALA 737 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.158 ? 
metalc ? metalc12 A OD2 ASP 708 A ASP 756 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? 
metalc ? metalc13 A OE1 GLU 747 A GLU 795 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.199 ? 
#
_chem_comp.formula           'C18 H19 N3 O2' 
_chem_comp.formula_weight    309.362 
_chem_comp.id                J3C 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol 
_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
O1 C6 J3C sing 191 n n 
O2 C11 J3C sing 192 n n 
C6 C3 J3C sing 193 n n 
C6 C11 J3C sing 194 n n 
C2 C3 J3C sing 195 n y 
C2 C1 J3C doub 196 n y 
C3 C4 J3C doub 197 n y 
C11 C12 J3C sing 198 n n 
C1 N1 J3C sing 199 n y 
C4 N3 J3C sing 200 n n 
C4 C5 J3C sing 201 n y 
N1 C5 J3C sing 202 n y 
N1 C8 J3C sing 203 n y 
C18 C17 J3C doub 204 n y 
C18 C13 J3C sing 205 n y 
C12 N3 J3C sing 206 n n 
C12 C13 J3C sing 207 n n 
C5 N2 J3C doub 208 n y 
C17 C16 J3C sing 209 n y 
C13 C14 J3C doub 210 n y 
C10 C8 J3C sing 211 n n 
C8 C7 J3C doub 212 n y 
N2 C7 J3C sing 213 n y 
C7 C9 J3C sing 214 n n 
C16 C15 J3C doub 215 n y 
C14 C15 J3C sing 216 n y 
C10 H1 J3C sing 217 n n 
C10 H2 J3C sing 218 n n 
C10 H3 J3C sing 219 n n 
C11 H4 J3C sing 220 n n 
C12 H5 J3C sing 221 n n 
C14 H6 J3C sing 222 n n 
C15 H7 J3C sing 223 n n 
C16 H8 J3C sing 224 n n 
C17 H9 J3C sing 225 n n 
C18 H10 J3C sing 226 n n 
C1 H11 J3C sing 227 n n 
C2 H12 J3C sing 228 n n 
C6 H13 J3C sing 229 n n 
C9 H14 J3C sing 230 n n 
C9 H15 J3C sing 231 n n 
C9 H16 J3C sing 232 n n 
N3 H17 J3C sing 233 n n 
O1 H18 J3C sing 234 n n 
O2 H19 J3C sing 235 n n 
#
_atom_sites.entry_id                     7EFN 
_atom_sites.fract_transf_matrix[1][1]    0.009439 
_atom_sites.fract_transf_matrix[1][2]    0.00545 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0109 
_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]    0.002688 
_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 3 MG A 1 1101 1102 MG MG . 
D 4 RB A 1 1102 1105 RB RB . 
E 4 RB A 1 1103 1106 RB RB . 
F 5 J3C A 1 1104 1 J3C BYK . 
G 4 RB A 1 1105 1 RB RB . 
H 4 RB A 1 1106 3 RB RB . 
I 6 NAG B 1 301 301 NAG NAG . 
J 6 NAG B 1 302 302 NAG NAG . 
K 6 NAG B 1 303 303 NAG NAG . 
L 7 HOH A 1 1201 44 HOH HOH . 
L 7 HOH A 2 1202 35 HOH HOH . 
L 7 HOH A 3 1203 4 HOH HOH . 
L 7 HOH A 4 1204 18 HOH HOH . 
L 7 HOH A 5 1205 13 HOH HOH . 
L 7 HOH A 6 1206 45 HOH HOH . 
L 7 HOH A 7 1207 28 HOH HOH . 
L 7 HOH A 8 1208 12 HOH HOH . 
L 7 HOH A 9 1209 33 HOH HOH . 
L 7 HOH A 10 1210 5 HOH HOH . 
L 7 HOH A 11 1211 42 HOH HOH . 
L 7 HOH A 12 1212 11 HOH HOH . 
L 7 HOH A 13 1213 3 HOH HOH . 
L 7 HOH A 14 1214 9 HOH HOH . 
L 7 HOH A 15 1215 26 HOH HOH . 
L 7 HOH A 16 1216 6 HOH HOH . 
L 7 HOH A 17 1217 21 HOH HOH . 
L 7 HOH A 18 1218 27 HOH HOH . 
L 7 HOH A 19 1219 25 HOH HOH . 
L 7 HOH A 20 1220 8 HOH HOH . 
L 7 HOH A 21 1221 43 HOH HOH . 
L 7 HOH A 22 1222 7 HOH HOH . 
L 7 HOH A 23 1223 10 HOH HOH . 
L 7 HOH A 24 1224 22 HOH HOH . 
L 7 HOH A 25 1225 14 HOH HOH . 
L 7 HOH A 26 1226 24 HOH HOH . 
L 7 HOH A 27 1227 36 HOH HOH . 
L 7 HOH A 28 1228 19 HOH HOH . 
L 7 HOH A 29 1229 38 HOH HOH . 
L 7 HOH A 30 1230 32 HOH HOH . 
L 7 HOH A 31 1231 17 HOH HOH . 
L 7 HOH A 32 1232 37 HOH HOH . 
L 7 HOH A 33 1233 30 HOH HOH . 
L 7 HOH A 34 1234 34 HOH HOH . 
L 7 HOH A 35 1235 39 HOH HOH . 
L 7 HOH A 36 1236 16 HOH HOH . 
M 7 HOH B 1 401 31 HOH HOH . 
M 7 HOH B 2 402 29 HOH HOH . 
M 7 HOH B 3 403 15 HOH HOH . 
M 7 HOH B 4 404 40 HOH HOH . 
M 7 HOH B 5 405 23 HOH HOH . 
M 7 HOH B 6 406 20 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 J3C . . . F 5 51.905 -10.816 -7.058 1 49.4 ? C10 J3C 1104 A 1 
HETATM 2 C C11 J3C . . . F 5 50.753 -17.916 -9.376 1 47.34 ? C11 J3C 1104 A 1 
HETATM 3 C C12 J3C . . . F 5 50.811 -17.974 -7.85 1 49.4 ? C12 J3C 1104 A 1 
HETATM 4 C C13 J3C . . . F 5 49.806 -18.873 -7.222 1 48.02 ? C13 J3C 1104 A 1 
HETATM 5 C C14 J3C . . . F 5 49.711 -18.866 -5.834 1 48.29 ? C14 J3C 1104 A 1 
HETATM 6 C C15 J3C . . . F 5 48.801 -19.687 -5.181 1 44.34 ? C15 J3C 1104 A 1 
HETATM 7 C C16 J3C . . . F 5 47.972 -20.522 -5.918 1 45.38 ? C16 J3C 1104 A 1 
HETATM 8 C C17 J3C . . . F 5 48.063 -20.537 -7.306 1 50.29 ? C17 J3C 1104 A 1 
HETATM 9 C C18 J3C . . . F 5 48.979 -19.718 -7.959 1 49.67 ? C18 J3C 1104 A 1 
HETATM 10 C C1 J3C . . . F 5 52.18 -13.283 -8.971 1 48.39 ? C1 J3C 1104 A 1 
HETATM 11 C C2 J3C . . . F 5 52.229 -14.468 -9.703 1 48.03 ? C2 J3C 1104 A 1 
HETATM 12 C C3 J3C . . . F 5 51.702 -15.63 -9.157 1 44.17 ? C3 J3C 1104 A 1 
HETATM 13 C C4 J3C . . . F 5 51.147 -15.565 -7.891 1 42.9 ? C4 J3C 1104 A 1 
HETATM 14 C C5 J3C . . . F 5 51.123 -14.363 -7.197 1 48.74 ? C5 J3C 1104 A 1 
HETATM 15 C C6 J3C . . . F 5 51.753 -16.9 -9.926 1 49.03 ? C6 J3C 1104 A 1 
HETATM 16 C C7 J3C . . . F 5 50.848 -12.761 -5.738 1 38.07 ? C7 J3C 1104 A 1 
HETATM 17 C C8 J3C . . . F 5 51.477 -12.247 -6.865 1 45.77 ? C8 J3C 1104 A 1 
HETATM 18 C C9 J3C . . . F 5 50.467 -12.003 -4.494 1 33.1 ? C9 J3C 1104 A 1 
HETATM 19 N N1 J3C . . . F 5 51.635 -13.249 -7.744 1 50.85 ? N1 J3C 1104 A 1 
HETATM 20 N N2 J3C . . . F 5 50.64 -14.07 -5.968 1 49.63 ? N2 J3C 1104 A 1 
HETATM 21 N N3 J3C . . . F 5 50.625 -16.651 -7.293 1 45.72 ? N3 J3C 1104 A 1 
HETATM 22 O O1 J3C . . . F 5 53.086 -17.429 -9.893 1 56.75 ? O1 J3C 1104 A 1 
HETATM 23 O O2 J3C . . . F 5 49.453 -17.511 -9.813 1 55.5 ? O2 J3C 1104 A 1 
#
_model_server_stats.io_time_ms              33 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           23 
#