data_7UMY
#
_model_server_result.job_id            P6mfBZgR7Eybd3Fj07BtKw 
_model_server_result.datetime_utc      '2024-12-11 07:26:32' 
_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          7umy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":301}' 
#
_entry.id    7UMY 
#
_exptl.entry_id    7UMY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.462 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.297 
_cell.angle_gamma         90 
_cell.entry_id            7UMY 
_cell.length_a            256.215 
_cell.length_b            79.137 
_cell.length_c            89.425 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7UMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 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
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,G,H,K,L,O,P,Q,R,S,U,W,X 1 1 
B,I,J,T 2 1,3 
D,M,N,V 2 2,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 -31.020329 0 83.872342 
3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -31.020329 0 83.872342 
4 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 I N N 
? 3 K N N 
? 3 N N N 
? 3 O N N 
? 3 Q 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
covale ? covale1 A N ILE 26 A ILE 22 1_555 G O2N NAD . A NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? 
covale ? covale2 A NZ LYS 170 A LYS 166 1_555 G O2D NAD . A NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale3 C N ILE 26 C ILE 22 1_555 L O2N NAD . C NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? 
covale ? covale4 C NZ LYS 170 C LYS 166 1_555 L O2D NAD . C NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale5 D N ILE 26 D ILE 22 1_555 M O2N NAD . D NAD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? 
covale ? covale6 F N ILE 26 F ILE 22 1_555 R O2N NAD . F NAD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? 
#
_chem_comp.formula           'C23 H24 N4 O3' 
_chem_comp.formula_weight    404.462 
_chem_comp.id                NUC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide 
_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
C13 N4 NUC sing 312 n n 
O1 C1 NUC doub 313 n n 
N4 C1 NUC sing 314 n n 
N4 C14 NUC sing 315 n n 
C1 C2 NUC sing 316 n n 
C17 C16 NUC sing 317 n n 
C2 C3 NUC doub 318 e n 
C14 C15 NUC sing 319 n n 
C3 C4 NUC sing 320 n n 
C16 C15 NUC doub 321 n y 
C16 C18 NUC sing 322 n y 
C15 O3 NUC sing 323 n y 
C18 C19 NUC doub 324 n y 
C18 C23 NUC sing 325 n y 
C5 C4 NUC doub 326 n y 
C5 N1 NUC sing 327 n y 
C19 C20 NUC sing 328 n y 
C4 C12 NUC sing 329 n y 
O3 C23 NUC sing 330 n y 
C23 C22 NUC doub 331 n y 
C20 C21 NUC doub 332 n y 
N1 C6 NUC doub 333 n y 
C22 C21 NUC sing 334 n y 
C12 C11 NUC doub 335 n y 
C6 C11 NUC sing 336 n y 
C6 N2 NUC sing 337 n n 
C11 C10 NUC sing 338 n n 
N2 C7 NUC sing 339 n n 
C10 C9 NUC sing 340 n n 
C8 C7 NUC sing 341 n n 
C8 C9 NUC sing 342 n n 
C8 N3 NUC sing 343 n n 
C7 O2 NUC doub 344 n n 
N3 H1 NUC sing 345 n n 
N3 H2 NUC sing 346 n n 
C2 H4 NUC sing 347 n n 
C5 H5 NUC sing 348 n n 
C10 H6 NUC sing 349 n n 
C10 H7 NUC sing 350 n n 
C12 H8 NUC sing 351 n n 
C13 H9 NUC sing 352 n n 
C13 H10 NUC sing 353 n n 
C13 H11 NUC sing 354 n n 
C14 H12 NUC sing 355 n n 
C14 H13 NUC sing 356 n n 
C17 H14 NUC sing 357 n n 
C17 H15 NUC sing 358 n n 
C17 H16 NUC sing 359 n n 
C19 H17 NUC sing 360 n n 
C20 H18 NUC sing 361 n n 
C21 H19 NUC sing 362 n n 
C22 H20 NUC sing 363 n n 
C3 H21 NUC sing 364 n n 
C8 H22 NUC sing 365 n n 
C9 H23 NUC sing 366 n n 
C9 H24 NUC sing 367 n n 
N2 H25 NUC sing 368 n n 
#
_atom_sites.entry_id                     7UMY 
_atom_sites.fract_transf_matrix[1][1]    0.003903 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001444 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012636 
_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]    0.011923 
_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 2 NAD A 1 301 301 NAD NAD . 
H 3 NUC A 1 302 302 NUC BRD . 
I 3 NUC B 1 301 301 NUC BRD . 
J 2 NAD B 1 302 302 NAD NAD . 
K 3 NUC C 1 301 301 NUC BRD . 
L 2 NAD C 1 302 302 NAD NAD . 
M 2 NAD D 1 301 301 NAD NAD . 
N 3 NUC D 1 302 302 NUC BRD . 
O 3 NUC E 1 301 301 NUC BRD . 
P 2 NAD E 1 302 302 NAD NAD . 
Q 3 NUC F 1 301 301 NUC BRD . 
R 2 NAD F 1 302 302 NAD NAD . 
S 4 HOH A 1 401 5 HOH HOH . 
S 4 HOH A 2 402 14 HOH HOH . 
S 4 HOH A 3 403 21 HOH HOH . 
S 4 HOH A 4 404 11 HOH HOH . 
T 4 HOH B 1 401 27 HOH HOH . 
T 4 HOH B 2 402 7 HOH HOH . 
U 4 HOH C 1 401 13 HOH HOH . 
U 4 HOH C 2 402 18 HOH HOH . 
U 4 HOH C 3 403 9 HOH HOH . 
U 4 HOH C 4 404 36 HOH HOH . 
U 4 HOH C 5 405 12 HOH HOH . 
U 4 HOH C 6 406 32 HOH HOH . 
U 4 HOH C 7 407 24 HOH HOH . 
U 4 HOH C 8 408 15 HOH HOH . 
U 4 HOH C 9 409 22 HOH HOH . 
V 4 HOH D 1 401 17 HOH HOH . 
W 4 HOH E 1 401 33 HOH HOH . 
W 4 HOH E 2 402 31 HOH HOH . 
X 4 HOH F 1 401 26 HOH HOH . 
X 4 HOH F 2 402 4 HOH HOH . 
X 4 HOH F 3 403 16 HOH HOH . 
X 4 HOH F 4 404 1 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 C4 NUC . . . Q 3 24.494 -9.832 -1.836 1 76.17 ? C4 NUC 301 F 1 
HETATM 2 N N3 NUC . . . Q 3 20.626 -6.211 -5.668 1 86.67 ? N3 NUC 301 F 1 
HETATM 3 C C2 NUC . . . Q 3 26.368 -11.428 -1.103 1 71.07 ? C2 NUC 301 F 1 
HETATM 4 N N1 NUC . . . Q 3 22.117 -10.195 -1.981 1 87.31 ? N1 NUC 301 F 1 
HETATM 5 C C7 NUC . . . Q 3 20.278 -7.792 -3.737 1 90.46 ? C7 NUC 301 F 1 
HETATM 6 C C6 NUC . . . Q 3 21.985 -8.939 -2.406 1 83.05 ? C6 NUC 301 F 1 
HETATM 7 O O2 NUC . . . Q 3 19.09 -7.55 -3.743 1 89.52 ? O2 NUC 301 F 1 
HETATM 8 C C5 NUC . . . Q 3 23.344 -10.64 -1.702 1 82.29 ? C5 NUC 301 F 1 
HETATM 9 C C1 NUC . . . Q 3 27.8 -11.612 -0.88 1 66.14 ? C1 NUC 301 F 1 
HETATM 10 C C10 NUC . . . Q 3 22.792 -6.647 -3.061 1 80.32 ? C10 NUC 301 F 1 
HETATM 11 C C11 NUC . . . Q 3 23.047 -8.059 -2.576 1 76.32 ? C11 NUC 301 F 1 
HETATM 12 C C12 NUC . . . Q 3 24.318 -8.515 -2.284 1 76.89 ? C12 NUC 301 F 1 
HETATM 13 C C13 NUC . . . Q 3 28.689 -9.971 -2.551 1 70.42 ? C13 NUC 301 F 1 
HETATM 14 C C14 NUC . . . Q 3 29.738 -10.192 -0.23 1 64.75 ? C14 NUC 301 F 1 
HETATM 15 C C15 NUC . . . Q 3 29.19 -9.112 0.685 1 67.85 ? C15 NUC 301 F 1 
HETATM 16 C C16 NUC . . . Q 3 29.856 -8.155 1.364 1 70.29 ? C16 NUC 301 F 1 
HETATM 17 C C17 NUC . . . Q 3 31.348 -7.941 1.358 1 74.39 ? C17 NUC 301 F 1 
HETATM 18 C C18 NUC . . . Q 3 28.905 -7.394 2.075 1 72.24 ? C18 NUC 301 F 1 
HETATM 19 C C19 NUC . . . Q 3 28.971 -6.29 2.94 1 78.9 ? C19 NUC 301 F 1 
HETATM 20 C C20 NUC . . . Q 3 27.79 -5.787 3.476 1 85.06 ? C20 NUC 301 F 1 
HETATM 21 C C21 NUC . . . Q 3 26.545 -6.372 3.159 1 83.95 ? C21 NUC 301 F 1 
HETATM 22 C C22 NUC . . . Q 3 26.481 -7.465 2.302 1 80.77 ? C22 NUC 301 F 1 
HETATM 23 C C23 NUC . . . Q 3 27.676 -7.952 1.775 1 74.07 ? C23 NUC 301 F 1 
HETATM 24 C C3 NUC . . . Q 3 25.868 -10.237 -1.549 1 77.35 ? C3 NUC 301 F 1 
HETATM 25 C C8 NUC . . . Q 3 21.2 -7.339 -4.896 1 93.5 ? C8 NUC 301 F 1 
HETATM 26 C C9 NUC . . . Q 3 22.566 -6.701 -4.571 1 92.61 ? C9 NUC 301 F 1 
HETATM 27 N N2 NUC . . . Q 3 20.707 -8.525 -2.681 1 90 ? N2 NUC 301 F 1 
HETATM 28 N N4 NUC . . . Q 3 28.692 -10.599 -1.212 1 64.62 ? N4 NUC 301 F 1 
HETATM 29 O O1 NUC . . . Q 3 28.269 -12.645 -0.404 1 64.03 ? O1 NUC 301 F 1 
HETATM 30 O O3 NUC . . . Q 3 27.841 -9.011 0.919 1 69.88 ? O3 NUC 301 F 1 
HETATM 31 H H1 NUC . . . Q 3 20.833 -6.308 -6.654 1 105.41 ? H1 NUC 301 F 1 
HETATM 32 H H2 NUC . . . Q 3 19.621 -6.205 -5.551 1 105.41 ? H2 NUC 301 F 1 
HETATM 33 H H4 NUC . . . Q 3 25.742 -12.253 -0.905 1 86.69 ? H4 NUC 301 F 1 
HETATM 34 H H5 NUC . . . Q 3 23.431 -11.64 -1.369 1 100.15 ? H5 NUC 301 F 1 
HETATM 35 H H6 NUC . . . Q 3 23.645 -6.004 -2.841 1 97.79 ? H6 NUC 301 F 1 
HETATM 36 H H7 NUC . . . Q 3 21.912 -6.224 -2.574 1 97.79 ? H7 NUC 301 F 1 
HETATM 37 H H8 NUC . . . Q 3 25.16 -7.881 -2.396 1 93.67 ? H8 NUC 301 F 1 
HETATM 38 H H9 NUC . . . Q 3 28.048 -10.553 -3.2 1 85.91 ? H9 NUC 301 F 1 
HETATM 39 H H10 NUC . . . Q 3 29.704 -9.964 -2.927 1 85.91 ? H10 NUC 301 F 1 
HETATM 40 H H11 NUC . . . Q 3 28.314 -8.961 -2.453 1 85.91 ? H11 NUC 301 F 1 
HETATM 41 H H12 NUC . . . Q 3 30.012 -11.033 0.394 1 79.1 ? H12 NUC 301 F 1 
HETATM 42 H H13 NUC . . . Q 3 30.592 -9.772 -0.747 1 79.1 ? H13 NUC 301 F 1 
HETATM 43 H H14 NUC . . . Q 3 31.754 -8.377 2.271 1 90.68 ? H14 NUC 301 F 1 
HETATM 44 H H15 NUC . . . Q 3 31.534 -6.867 1.325 1 90.68 ? H15 NUC 301 F 1 
HETATM 45 H H16 NUC . . . Q 3 31.756 -8.434 0.476 1 90.68 ? H16 NUC 301 F 1 
HETATM 46 H H17 NUC . . . Q 3 29.906 -5.852 3.178 1 96.08 ? H17 NUC 301 F 1 
HETATM 47 H H18 NUC . . . Q 3 27.821 -4.954 4.131 1 103.48 ? H18 NUC 301 F 1 
HETATM 48 H H19 NUC . . . Q 3 25.657 -5.974 3.577 1 102.15 ? H19 NUC 301 F 1 
HETATM 49 H H20 NUC . . . Q 3 25.559 -7.921 2.051 1 98.33 ? H20 NUC 301 F 1 
HETATM 50 H H21 NUC . . . Q 3 26.577 -9.465 -1.723 1 94.23 ? H21 NUC 301 F 1 
HETATM 51 H H22 NUC . . . Q 3 21.314 -8.258 -5.457 1 113.61 ? H22 NUC 301 F 1 
HETATM 52 H H23 NUC . . . Q 3 23.356 -7.29 -5.039 1 112.54 ? H23 NUC 301 F 1 
HETATM 53 H H24 NUC . . . Q 3 22.595 -5.69 -4.982 1 112.54 ? H24 NUC 301 F 1 
HETATM 54 H H25 NUC . . . Q 3 19.987 -8.802 -2.005 1 109.41 ? H25 NUC 301 F 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    63 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           54 
#