data_3EEJ
#
_model_server_result.job_id            TaKAtvw4crUFK0ddkUl7oQ 
_model_server_result.datetime_utc      '2024-11-07 10:32:50' 
_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          3eej 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":229}' 
#
_entry.id    3EEJ 
#
_exptl.entry_id    3EEJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              358.436 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine 
_entity.pdbx_number_of_molecules    2 
_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            3EEJ 
_cell.length_a            42.871 
_cell.length_b            42.871 
_cell.length_c            231.485 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EEJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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 D N N 
? 3 F N N 
#
_chem_comp.formula           'C22 H22 N4 O' 
_chem_comp.formula_weight    358.436 
_chem_comp.id                53R 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine 
_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
C20 C21 53R doub 1 n y 
C20 C25 53R sing 2 n y 
C21 C22 53R sing 3 n y 
C22 C23 53R doub 4 n y 
C23 C24 53R sing 5 n y 
C24 C25 53R doub 6 n y 
C25 C18 53R sing 7 n y 
C18 C19 53R doub 8 n y 
C18 C17 53R sing 9 n y 
C19 C14 53R sing 10 n y 
C17 C16 53R doub 11 n y 
C16 O17 53R sing 12 n n 
C16 C15 53R sing 13 n y 
O17 C2 53R sing 14 n n 
C15 C14 53R doub 15 n y 
C14 C12 53R sing 16 n n 
C12 C13 53R sing 17 n n 
C12 C11 53R sing 18 n n 
C11 C10 53R trip 19 n n 
C10 C6 53R sing 20 n n 
C6 C5 53R doub 21 n y 
C6 C1 53R sing 22 n y 
C5 C8 53R sing 23 n n 
C5 N4 53R sing 24 n y 
N4 C3 53R doub 25 n y 
C3 N7 53R sing 26 n n 
C3 N2 53R sing 27 n y 
N2 C1 53R doub 28 n y 
C1 N9 53R sing 29 n n 
C20 H20 53R sing 30 n n 
C21 H21 53R sing 31 n n 
C22 H22 53R sing 32 n n 
C23 H23 53R sing 33 n n 
C24 H24 53R sing 34 n n 
C19 H19 53R sing 35 n n 
C17 H17 53R sing 36 n n 
C2 H2 53R sing 37 n n 
C2 H2A 53R sing 38 n n 
C2 H2B 53R sing 39 n n 
C15 H15 53R sing 40 n n 
C12 H12 53R sing 41 n n 
C13 H13 53R sing 42 n n 
C13 H13A 53R sing 43 n n 
C13 H13B 53R sing 44 n n 
C8 H8 53R sing 45 n n 
C8 H8A 53R sing 46 n n 
C8 H8B 53R sing 47 n n 
N7 HN7 53R sing 48 n n 
N7 HN7A 53R sing 49 n n 
N9 HN9 53R sing 50 n n 
N9 HN9A 53R sing 51 n n 
#
_atom_sites.entry_id                     3EEJ 
_atom_sites.fract_transf_matrix[1][1]    0.023326 
_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]    0.023326 
_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]    0.00432 
_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 NDP A 1 228 228 NDP NAP . 
D 3 53R A 1 229 1 53R 53R . 
E 2 NDP B 1 228 228 NDP NAP . 
F 3 53R B 1 229 2 53R 53R . 
G 4 HOH A 1 230 1 HOH HOH . 
G 4 HOH A 2 231 3 HOH HOH . 
G 4 HOH A 3 232 6 HOH HOH . 
G 4 HOH A 4 233 7 HOH HOH . 
G 4 HOH A 5 234 13 HOH HOH . 
G 4 HOH A 6 235 14 HOH HOH . 
G 4 HOH A 7 236 15 HOH HOH . 
G 4 HOH A 8 237 17 HOH HOH . 
G 4 HOH A 9 238 18 HOH HOH . 
G 4 HOH A 10 239 20 HOH HOH . 
G 4 HOH A 11 240 25 HOH HOH . 
G 4 HOH A 12 241 26 HOH HOH . 
G 4 HOH A 13 242 27 HOH HOH . 
G 4 HOH A 14 243 28 HOH HOH . 
G 4 HOH A 15 244 30 HOH HOH . 
G 4 HOH A 16 245 32 HOH HOH . 
G 4 HOH A 17 246 33 HOH HOH . 
G 4 HOH A 18 247 34 HOH HOH . 
G 4 HOH A 19 248 39 HOH HOH . 
G 4 HOH A 20 249 42 HOH HOH . 
G 4 HOH A 21 250 44 HOH HOH . 
G 4 HOH A 22 251 45 HOH HOH . 
G 4 HOH A 23 252 46 HOH HOH . 
G 4 HOH A 24 253 50 HOH HOH . 
G 4 HOH A 25 254 51 HOH HOH . 
G 4 HOH A 26 255 52 HOH HOH . 
G 4 HOH A 27 256 53 HOH HOH . 
G 4 HOH A 28 257 54 HOH HOH . 
G 4 HOH A 29 258 56 HOH HOH . 
G 4 HOH A 30 259 58 HOH HOH . 
G 4 HOH A 31 260 59 HOH HOH . 
G 4 HOH A 32 261 62 HOH HOH . 
G 4 HOH A 33 262 66 HOH HOH . 
G 4 HOH A 34 263 68 HOH HOH . 
G 4 HOH A 35 264 74 HOH HOH . 
G 4 HOH A 36 265 76 HOH HOH . 
G 4 HOH A 37 266 81 HOH HOH . 
G 4 HOH A 38 267 83 HOH HOH . 
G 4 HOH A 39 268 85 HOH HOH . 
G 4 HOH A 40 269 87 HOH HOH . 
G 4 HOH A 41 270 88 HOH HOH . 
G 4 HOH A 42 271 89 HOH HOH . 
G 4 HOH A 43 272 91 HOH HOH . 
G 4 HOH A 44 273 95 HOH HOH . 
G 4 HOH A 45 274 96 HOH HOH . 
G 4 HOH A 46 275 97 HOH HOH . 
G 4 HOH A 47 276 99 HOH HOH . 
G 4 HOH A 48 277 102 HOH HOH . 
G 4 HOH A 49 278 103 HOH HOH . 
G 4 HOH A 50 279 106 HOH HOH . 
G 4 HOH A 51 280 107 HOH HOH . 
G 4 HOH A 52 281 109 HOH HOH . 
G 4 HOH A 53 282 110 HOH HOH . 
G 4 HOH A 54 283 116 HOH HOH . 
G 4 HOH A 55 284 117 HOH HOH . 
G 4 HOH A 56 285 119 HOH HOH . 
G 4 HOH A 57 286 121 HOH HOH . 
G 4 HOH A 58 287 122 HOH HOH . 
G 4 HOH A 59 288 123 HOH HOH . 
G 4 HOH A 60 289 124 HOH HOH . 
G 4 HOH A 61 290 126 HOH HOH . 
G 4 HOH A 62 291 132 HOH HOH . 
G 4 HOH A 63 292 134 HOH HOH . 
G 4 HOH A 64 293 138 HOH HOH . 
G 4 HOH A 65 294 139 HOH HOH . 
G 4 HOH A 66 295 140 HOH HOH . 
G 4 HOH A 67 296 141 HOH HOH . 
G 4 HOH A 68 297 144 HOH HOH . 
G 4 HOH A 69 298 145 HOH HOH . 
G 4 HOH A 70 299 147 HOH HOH . 
G 4 HOH A 71 300 148 HOH HOH . 
G 4 HOH A 72 301 150 HOH HOH . 
G 4 HOH A 73 302 154 HOH HOH . 
G 4 HOH A 74 303 157 HOH HOH . 
G 4 HOH A 75 304 158 HOH HOH . 
G 4 HOH A 76 305 160 HOH HOH . 
G 4 HOH A 77 306 161 HOH HOH . 
G 4 HOH A 78 307 163 HOH HOH . 
G 4 HOH A 79 308 166 HOH HOH . 
G 4 HOH A 80 309 170 HOH HOH . 
G 4 HOH A 81 310 173 HOH HOH . 
G 4 HOH A 82 311 174 HOH HOH . 
G 4 HOH A 83 312 176 HOH HOH . 
G 4 HOH A 84 313 177 HOH HOH . 
G 4 HOH A 85 314 178 HOH HOH . 
G 4 HOH A 86 315 183 HOH HOH . 
G 4 HOH A 87 316 184 HOH HOH . 
G 4 HOH A 88 317 186 HOH HOH . 
G 4 HOH A 89 318 187 HOH HOH . 
G 4 HOH A 90 319 188 HOH HOH . 
G 4 HOH A 91 320 190 HOH HOH . 
G 4 HOH A 92 321 37 HOH HOH . 
H 4 HOH B 1 230 2 HOH HOH . 
H 4 HOH B 2 231 4 HOH HOH . 
H 4 HOH B 3 232 5 HOH HOH . 
H 4 HOH B 4 233 8 HOH HOH . 
H 4 HOH B 5 234 9 HOH HOH . 
H 4 HOH B 6 235 10 HOH HOH . 
H 4 HOH B 7 236 11 HOH HOH . 
H 4 HOH B 8 237 12 HOH HOH . 
H 4 HOH B 9 238 16 HOH HOH . 
H 4 HOH B 10 239 19 HOH HOH . 
H 4 HOH B 11 240 21 HOH HOH . 
H 4 HOH B 12 241 22 HOH HOH . 
H 4 HOH B 13 242 23 HOH HOH . 
H 4 HOH B 14 243 24 HOH HOH . 
H 4 HOH B 15 244 29 HOH HOH . 
H 4 HOH B 16 245 31 HOH HOH . 
H 4 HOH B 17 246 35 HOH HOH . 
H 4 HOH B 18 247 36 HOH HOH . 
H 4 HOH B 19 249 38 HOH HOH . 
H 4 HOH B 20 250 40 HOH HOH . 
H 4 HOH B 21 251 41 HOH HOH . 
H 4 HOH B 22 252 43 HOH HOH . 
H 4 HOH B 23 253 47 HOH HOH . 
H 4 HOH B 24 254 48 HOH HOH . 
H 4 HOH B 25 255 49 HOH HOH . 
H 4 HOH B 26 256 55 HOH HOH . 
H 4 HOH B 27 257 57 HOH HOH . 
H 4 HOH B 28 258 60 HOH HOH . 
H 4 HOH B 29 259 61 HOH HOH . 
H 4 HOH B 30 260 63 HOH HOH . 
H 4 HOH B 31 261 64 HOH HOH . 
H 4 HOH B 32 262 65 HOH HOH . 
H 4 HOH B 33 263 67 HOH HOH . 
H 4 HOH B 34 264 69 HOH HOH . 
H 4 HOH B 35 265 70 HOH HOH . 
H 4 HOH B 36 266 71 HOH HOH . 
H 4 HOH B 37 267 72 HOH HOH . 
H 4 HOH B 38 268 73 HOH HOH . 
H 4 HOH B 39 269 75 HOH HOH . 
H 4 HOH B 40 270 77 HOH HOH . 
H 4 HOH B 41 271 78 HOH HOH . 
H 4 HOH B 42 272 79 HOH HOH . 
H 4 HOH B 43 273 80 HOH HOH . 
H 4 HOH B 44 274 82 HOH HOH . 
H 4 HOH B 45 275 84 HOH HOH . 
H 4 HOH B 46 276 86 HOH HOH . 
H 4 HOH B 47 277 90 HOH HOH . 
H 4 HOH B 48 278 92 HOH HOH . 
H 4 HOH B 49 279 93 HOH HOH . 
H 4 HOH B 50 280 94 HOH HOH . 
H 4 HOH B 51 281 98 HOH HOH . 
H 4 HOH B 52 282 100 HOH HOH . 
H 4 HOH B 53 283 101 HOH HOH . 
H 4 HOH B 54 284 104 HOH HOH . 
H 4 HOH B 55 285 105 HOH HOH . 
H 4 HOH B 56 286 108 HOH HOH . 
H 4 HOH B 57 287 111 HOH HOH . 
H 4 HOH B 58 288 112 HOH HOH . 
H 4 HOH B 59 289 113 HOH HOH . 
H 4 HOH B 60 290 114 HOH HOH . 
H 4 HOH B 61 291 115 HOH HOH . 
H 4 HOH B 62 292 118 HOH HOH . 
H 4 HOH B 63 293 120 HOH HOH . 
H 4 HOH B 64 294 125 HOH HOH . 
H 4 HOH B 65 295 127 HOH HOH . 
H 4 HOH B 66 296 128 HOH HOH . 
H 4 HOH B 67 297 129 HOH HOH . 
H 4 HOH B 68 298 130 HOH HOH . 
H 4 HOH B 69 299 131 HOH HOH . 
H 4 HOH B 70 300 133 HOH HOH . 
H 4 HOH B 71 301 135 HOH HOH . 
H 4 HOH B 72 302 136 HOH HOH . 
H 4 HOH B 73 303 137 HOH HOH . 
H 4 HOH B 74 304 142 HOH HOH . 
H 4 HOH B 75 305 143 HOH HOH . 
H 4 HOH B 76 306 146 HOH HOH . 
H 4 HOH B 77 307 149 HOH HOH . 
H 4 HOH B 78 308 151 HOH HOH . 
H 4 HOH B 79 309 152 HOH HOH . 
H 4 HOH B 80 310 153 HOH HOH . 
H 4 HOH B 81 311 155 HOH HOH . 
H 4 HOH B 82 312 156 HOH HOH . 
H 4 HOH B 83 313 159 HOH HOH . 
H 4 HOH B 84 314 162 HOH HOH . 
H 4 HOH B 85 315 164 HOH HOH . 
H 4 HOH B 86 316 165 HOH HOH . 
H 4 HOH B 87 317 167 HOH HOH . 
H 4 HOH B 88 318 168 HOH HOH . 
H 4 HOH B 89 319 169 HOH HOH . 
H 4 HOH B 90 320 171 HOH HOH . 
H 4 HOH B 91 321 172 HOH HOH . 
H 4 HOH B 92 322 175 HOH HOH . 
H 4 HOH B 93 323 179 HOH HOH . 
H 4 HOH B 94 324 180 HOH HOH . 
H 4 HOH B 95 325 181 HOH HOH . 
H 4 HOH B 96 326 182 HOH HOH . 
H 4 HOH B 97 327 185 HOH HOH . 
H 4 HOH B 98 328 189 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 C20 53R . . . F 3 26.734 12.506 37.638 1 26.97 ? C20 53R 229 B 1 
HETATM 2 C C21 53R . . . F 3 27.163 13.572 38.456 1 28.92 ? C21 53R 229 B 1 
HETATM 3 C C22 53R . . . F 3 26.915 13.546 39.85 1 28.04 ? C22 53R 229 B 1 
HETATM 4 C C23 53R . . . F 3 26.229 12.46 40.422 1 26.75 ? C23 53R 229 B 1 
HETATM 5 C C24 53R . . . F 3 25.799 11.399 39.6 1 26.51 ? C24 53R 229 B 1 
HETATM 6 C C25 53R . . . F 3 26.043 11.426 38.213 1 22.6 ? C25 53R 229 B 1 
HETATM 7 C C18 53R . . . F 3 25.611 10.38 37.396 1 24.4 ? C18 53R 229 B 1 
HETATM 8 C C19 53R . . . F 3 26.389 10.009 36.279 1 21.76 ? C19 53R 229 B 1 
HETATM 9 C C17 53R . . . F 3 24.417 9.674 37.693 1 22.94 ? C17 53R 229 B 1 
HETATM 10 C C16 53R . . . F 3 23.952 8.62 36.89 1 22.8 ? C16 53R 229 B 1 
HETATM 11 O O17 53R . . . F 3 22.753 7.892 37.125 1 25.16 ? O17 53R 229 B 1 
HETATM 12 C C2 53R . . . F 3 22.612 6.595 36.475 1 14.01 ? C2 53R 229 B 1 
HETATM 13 C C15 53R . . . F 3 24.721 8.289 35.795 1 20.93 ? C15 53R 229 B 1 
HETATM 14 C C14 53R . . . F 3 25.883 8.957 35.511 1 18.98 ? C14 53R 229 B 1 
HETATM 15 C C12 53R . . . F 3 26.478 8.419 34.292 1 14.44 ? C12 53R 229 B 1 
HETATM 16 C C13 53R . . . F 3 26.344 9.341 33.077 1 14.68 ? C13 53R 229 B 1 
HETATM 17 C C11 53R . . . F 3 27.761 7.726 34.572 1 13.35 ? C11 53R 229 B 1 
HETATM 18 C C10 53R . . . F 3 28.75 7.073 34.675 1 10.83 ? C10 53R 229 B 1 
HETATM 19 C C6 53R . . . F 3 29.935 6.284 34.721 1 11.29 ? C6 53R 229 B 1 
HETATM 20 C C5 53R . . . F 3 30.611 6.148 35.949 1 11.21 ? C5 53R 229 B 1 
HETATM 21 C C8 53R . . . F 3 30.093 6.805 37.267 1 10.4 ? C8 53R 229 B 1 
HETATM 22 N N4 53R . . . F 3 31.739 5.421 35.97 1 10.47 ? N4 53R 229 B 1 
HETATM 23 C C3 53R . . . F 3 32.224 4.797 34.872 1 10.02 ? C3 53R 229 B 1 
HETATM 24 N N7 53R . . . F 3 33.376 4.086 34.977 1 10.63 ? N7 53R 229 B 1 
HETATM 25 N N2 53R . . . F 3 31.623 4.956 33.685 1 9.31 ? N2 53R 229 B 1 
HETATM 26 C C1 53R . . . F 3 30.467 5.659 33.558 1 10.99 ? C1 53R 229 B 1 
HETATM 27 N N9 53R . . . F 3 29.878 5.76 32.368 1 7.11 ? N9 53R 229 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           220 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#