data_8GKF
#
_model_server_result.job_id            OGh0tKNKlWE4PhWwpXdMYA 
_model_server_result.datetime_utc      '2024-11-13 05:30:09' 
_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          8gkf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":301}' 
#
_entry.id    8GKF 
#
_exptl.entry_id    8GKF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              458.488 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            TOMUDEX 
_entity.pdbx_number_of_molecules    9 
_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            8GKF 
_cell.length_a            141.83 
_cell.length_b            141.83 
_cell.length_c            209.745 
_cell.Z_PDB               72 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GKF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    'P 4abw 2nw' 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
PISA monomeric 1 author_and_software_defined_assembly 5 
PISA monomeric 1 author_and_software_defined_assembly 6 
PISA monomeric 1 author_and_software_defined_assembly 7 
PISA monomeric 1 author_and_software_defined_assembly 8 
PISA monomeric 1 author_and_software_defined_assembly 9 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,J,S 1 1 
B,K,T 2 1 
C,L,U 3 1 
D,M,V 4 1 
E,N,W 5 1 
F,O,X 6 1 
G,P,Y 7 1 
H,Q,Z 8 1 
I,R,AA 9 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
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
#
_chem_comp.formula           'C21 H22 N4 O6 S' 
_chem_comp.formula_weight    458.488 
_chem_comp.id                D16 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              TOMUDEX 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ZD1694;Raltitrexed 
#
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
N1 C2 D16 sing 83 n n 
N1 C8A D16 sing 84 n n 
N1 HN1 D16 sing 85 n n 
C2 CM2 D16 sing 86 n n 
C2 N3 D16 doub 87 n n 
CM2 HM21 D16 sing 88 n n 
CM2 HM22 D16 sing 89 n n 
CM2 HM23 D16 sing 90 n n 
N3 C4 D16 sing 91 n n 
C4 O4 D16 doub 92 n n 
C4 C4A D16 sing 93 n n 
C4A C5 D16 doub 94 n y 
C4A C8A D16 sing 95 n y 
C5 C6 D16 sing 96 n y 
C5 H5 D16 sing 97 n n 
C6 C7 D16 doub 98 n y 
C6 C9 D16 sing 99 n n 
C7 C8 D16 sing 100 n y 
C7 H7 D16 sing 101 n n 
C8 C8A D16 doub 102 n y 
C8 H8 D16 sing 103 n n 
C9 N10 D16 sing 104 n n 
C9 H91 D16 sing 105 n n 
C9 H92 D16 sing 106 n n 
N10 C14 D16 sing 107 n n 
N10 CP1 D16 sing 108 n n 
C11 S13 D16 sing 109 n y 
C11 C16 D16 doub 110 n y 
C11 C D16 sing 111 n n 
S13 C14 D16 sing 112 n y 
C14 C15 D16 doub 113 n y 
C15 C16 D16 sing 114 n y 
C15 H15 D16 sing 115 n n 
C16 H16 D16 sing 116 n n 
C O D16 doub 117 n n 
C N D16 sing 118 n n 
N CA D16 sing 119 n n 
N HN D16 sing 120 n n 
CA CB D16 sing 121 n n 
CA CT D16 sing 122 n n 
CA HA D16 sing 123 n n 
CB CG D16 sing 124 n n 
CB HB1 D16 sing 125 n n 
CB HB2 D16 sing 126 n n 
CG CD D16 sing 127 n n 
CG HG1 D16 sing 128 n n 
CG HG2 D16 sing 129 n n 
CD OE1 D16 doub 130 n n 
CD OE2 D16 sing 131 n n 
OE2 HOE2 D16 sing 132 n n 
CT O1 D16 doub 133 n n 
CT O2 D16 sing 134 n n 
O2 HO2 D16 sing 135 n n 
CP1 HP11 D16 sing 136 n n 
CP1 HP12 D16 sing 137 n n 
CP1 HP13 D16 sing 138 n n 
#
_atom_sites.entry_id                     8GKF 
_atom_sites.fract_transf_matrix[1][1]    0.007051 
_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]    0.007051 
_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]    0.004768 
_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
J 2 D16 A 1 301 301 D16 RAL . 
K 2 D16 B 1 301 301 D16 RAL . 
L 2 D16 C 1 301 301 D16 RAL . 
M 2 D16 D 1 301 301 D16 RAL . 
N 2 D16 E 1 301 301 D16 RAL . 
O 2 D16 F 1 301 301 D16 RAL . 
P 2 D16 G 1 301 301 D16 RAL . 
Q 2 D16 H 1 301 301 D16 RAL . 
R 2 D16 I 1 301 301 D16 RAL . 
S 3 HOH A 1 401 41 HOH HOH . 
S 3 HOH A 2 402 12 HOH HOH . 
S 3 HOH A 3 403 39 HOH HOH . 
S 3 HOH A 4 404 36 HOH HOH . 
S 3 HOH A 5 405 11 HOH HOH . 
S 3 HOH A 6 406 53 HOH HOH . 
S 3 HOH A 7 407 40 HOH HOH . 
S 3 HOH A 8 408 18 HOH HOH . 
S 3 HOH A 9 409 8 HOH HOH . 
S 3 HOH A 10 410 42 HOH HOH . 
S 3 HOH A 11 411 13 HOH HOH . 
T 3 HOH B 1 401 44 HOH HOH . 
T 3 HOH B 2 402 21 HOH HOH . 
T 3 HOH B 3 403 14 HOH HOH . 
T 3 HOH B 4 404 71 HOH HOH . 
T 3 HOH B 5 405 23 HOH HOH . 
T 3 HOH B 6 406 2 HOH HOH . 
T 3 HOH B 7 407 22 HOH HOH . 
T 3 HOH B 8 408 61 HOH HOH . 
T 3 HOH B 9 409 1 HOH HOH . 
T 3 HOH B 10 410 33 HOH HOH . 
T 3 HOH B 11 411 46 HOH HOH . 
T 3 HOH B 12 412 10 HOH HOH . 
T 3 HOH B 13 413 3 HOH HOH . 
T 3 HOH B 14 414 45 HOH HOH . 
T 3 HOH B 15 415 9 HOH HOH . 
T 3 HOH B 16 416 47 HOH HOH . 
T 3 HOH B 17 417 20 HOH HOH . 
T 3 HOH B 18 418 62 HOH HOH . 
T 3 HOH B 19 419 19 HOH HOH . 
T 3 HOH B 20 420 24 HOH HOH . 
U 3 HOH C 1 401 7 HOH HOH . 
U 3 HOH C 2 402 4 HOH HOH . 
U 3 HOH C 3 403 48 HOH HOH . 
U 3 HOH C 4 404 32 HOH HOH . 
U 3 HOH C 5 405 35 HOH HOH . 
U 3 HOH C 6 406 34 HOH HOH . 
V 3 HOH D 1 401 52 HOH HOH . 
V 3 HOH D 2 402 29 HOH HOH . 
V 3 HOH D 3 403 5 HOH HOH . 
V 3 HOH D 4 404 51 HOH HOH . 
V 3 HOH D 5 405 49 HOH HOH . 
V 3 HOH D 6 406 43 HOH HOH . 
V 3 HOH D 7 407 50 HOH HOH . 
W 3 HOH E 1 401 15 HOH HOH . 
W 3 HOH E 2 402 6 HOH HOH . 
W 3 HOH E 3 403 74 HOH HOH . 
W 3 HOH E 4 404 75 HOH HOH . 
W 3 HOH E 5 405 55 HOH HOH . 
W 3 HOH E 6 406 16 HOH HOH . 
W 3 HOH E 7 407 72 HOH HOH . 
W 3 HOH E 8 408 76 HOH HOH . 
X 3 HOH F 1 401 37 HOH HOH . 
X 3 HOH F 2 402 25 HOH HOH . 
X 3 HOH F 3 403 38 HOH HOH . 
Y 3 HOH G 1 401 54 HOH HOH . 
Y 3 HOH G 2 402 56 HOH HOH . 
Y 3 HOH G 3 403 17 HOH HOH . 
Y 3 HOH G 4 404 66 HOH HOH . 
Y 3 HOH G 5 405 30 HOH HOH . 
Y 3 HOH G 6 406 67 HOH HOH . 
Y 3 HOH G 7 407 64 HOH HOH . 
Y 3 HOH G 8 408 63 HOH HOH . 
Y 3 HOH G 9 409 65 HOH HOH . 
Z 3 HOH H 1 401 73 HOH HOH . 
Z 3 HOH H 2 402 26 HOH HOH . 
Z 3 HOH H 3 403 27 HOH HOH . 
Z 3 HOH H 4 404 68 HOH HOH . 
Z 3 HOH H 5 405 59 HOH HOH . 
Z 3 HOH H 6 406 28 HOH HOH . 
Z 3 HOH H 7 407 57 HOH HOH . 
Z 3 HOH H 8 408 58 HOH HOH . 
Z 3 HOH H 9 409 69 HOH HOH . 
Z 3 HOH H 10 410 70 HOH HOH . 
AA 3 HOH I 1 401 31 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 N N1 D16 . . . J 2 -46.099 -5.252 4.402 1 27.03 ? N1 D16 301 A 1 
HETATM 2 C C2 D16 . . . J 2 -45.958 -6.594 4.566 1 24.5 ? C2 D16 301 A 1 
HETATM 3 C CM2 D16 . . . J 2 -47.211 -7.405 4.603 1 21.09 ? CM2 D16 301 A 1 
HETATM 4 N N3 D16 . . . J 2 -44.802 -7.171 4.697 1 27.82 ? N3 D16 301 A 1 
HETATM 5 C C4 D16 . . . J 2 -43.661 -6.419 4.673 1 31.89 ? C4 D16 301 A 1 
HETATM 6 O O4 D16 . . . J 2 -42.58 -7.015 4.798 1 30.8 ? O4 D16 301 A 1 
HETATM 7 C C4A D16 . . . J 2 -43.731 -4.961 4.498 1 29.19 ? C4A D16 301 A 1 
HETATM 8 C C5 D16 . . . J 2 -42.608 -4.123 4.459 1 30.62 ? C5 D16 301 A 1 
HETATM 9 C C6 D16 . . . J 2 -42.742 -2.774 4.289 1 30.11 ? C6 D16 301 A 1 
HETATM 10 C C7 D16 . . . J 2 -44.042 -2.223 4.158 1 21.32 ? C7 D16 301 A 1 
HETATM 11 C C8 D16 . . . J 2 -45.157 -3.021 4.196 1 19.87 ? C8 D16 301 A 1 
HETATM 12 C C8A D16 . . . J 2 -45.01 -4.399 4.368 1 25.71 ? C8A D16 301 A 1 
HETATM 13 C C9 D16 . . . J 2 -41.531 -1.873 4.257 1 31.19 ? C9 D16 301 A 1 
HETATM 14 N N10 D16 . . . J 2 -41.237 -1.292 5.564 1 29.74 ? N10 D16 301 A 1 
HETATM 15 C C11 D16 . . . J 2 -42.736 1.687 7.362 1 24.95 ? C11 D16 301 A 1 
HETATM 16 S S13 D16 . . . J 2 -41.749 0.303 7.668 1 28.32 ? S13 D16 301 A 1 
HETATM 17 C C14 D16 . . . J 2 -41.82 -0.158 5.993 1 26.13 ? C14 D16 301 A 1 
HETATM 18 C C15 D16 . . . J 2 -42.526 0.774 5.233 1 26.01 ? C15 D16 301 A 1 
HETATM 19 C C16 D16 . . . J 2 -43.054 1.799 6.014 1 26.9 ? C16 D16 301 A 1 
HETATM 20 C C D16 . . . J 2 -43.102 2.538 8.523 1 33.47 ? C D16 301 A 1 
HETATM 21 O O D16 . . . J 2 -42.6 2.343 9.629 1 26.8 ? O D16 301 A 1 
HETATM 22 N N D16 . . . J 2 -43.992 3.513 8.3 1 33.53 ? N D16 301 A 1 
HETATM 23 C CA D16 . . . J 2 -44.374 4.434 9.355 1 30 ? CA D16 301 A 1 
HETATM 24 C CB D16 . . . J 2 -43.888 5.858 9.062 1 32.3 ? CB D16 301 A 1 
HETATM 25 C CG D16 . . . J 2 -44.267 6.333 7.671 1 27.67 ? CG D16 301 A 1 
HETATM 26 C CD D16 . . . J 2 -43.813 7.744 7.341 1 28.25 ? CD D16 301 A 1 
HETATM 27 O OE1 D16 . . . J 2 -44.233 8.677 8.05 1 33.63 ? OE1 D16 301 A 1 
HETATM 28 O OE2 D16 . . . J 2 -43.035 7.903 6.379 1 28.17 ? OE2 D16 301 A 1 
HETATM 29 C CT D16 . . . J 2 -45.89 4.402 9.619 1 29.94 ? CT D16 301 A 1 
HETATM 30 O O1 D16 . . . J 2 -46.504 3.377 9.269 1 38.31 ? O1 D16 301 A 1 
HETATM 31 O O2 D16 . . . J 2 -46.405 5.409 10.149 1 25.75 ? O2 D16 301 A 1 
HETATM 32 C CP1 D16 . . . J 2 -40.33 -2.023 6.43 1 34.44 ? CP1 D16 301 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           32 
#