data_4PY6
#
_model_server_result.job_id            2SgixIMG3KLr97CWPkQleg 
_model_server_result.datetime_utc      '2024-11-22 15:19:32' 
_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          4py6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1401}' 
#
_entry.id    4PY6 
#
_exptl.entry_id    4PY6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              521.654 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide 
_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            4PY6 
_cell.length_a            74.324 
_cell.length_b            84.269 
_cell.length_c            219.724 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PY6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 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 dimeric 2 software_defined_assembly 1 
PISA dimeric 2 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,E,F,J,L,N 1 1 
B,D,G,H,I,K,M,O 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
? 2 E N N 
? 2 G N N 
? 2 J N N 
? 2 K N N 
#
_chem_comp.formula           'C28 H39 N7 O3' 
_chem_comp.formula_weight    521.654 
_chem_comp.id                R78 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide 
_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
N1 C4 R78 doub 286 n y 
N1 C1 R78 sing 287 n y 
N3 C5 R78 sing 288 n n 
N3 C8 R78 sing 289 n n 
N3 C2 R78 sing 290 n n 
C4 C3 R78 sing 291 n y 
C5 C6 R78 sing 292 n n 
C5 C9 R78 sing 293 n n 
C6 O1 R78 doub 294 n n 
C6 N4 R78 sing 295 n n 
C7 C20 R78 doub 296 n y 
C7 C16 R78 sing 297 n y 
C7 N5 R78 sing 298 n n 
C8 C15 R78 sing 299 n n 
C8 C12 R78 sing 300 n n 
C10 C9 R78 sing 301 n n 
C13 C14 R78 sing 302 n n 
C13 C12 R78 sing 303 n n 
C15 C14 R78 sing 304 n n 
C17 C18 R78 sing 305 n y 
C17 C16 R78 doub 306 n y 
C20 C19 R78 sing 307 n y 
C21 O2 R78 doub 308 n n 
C21 N6 R78 sing 309 n n 
C21 C18 R78 sing 310 n n 
C22 N6 R78 sing 311 n n 
C22 C29 R78 sing 312 n n 
C22 C23 R78 sing 313 n n 
C24 N7 R78 sing 314 n n 
C24 C23 R78 sing 315 n n 
C28 C29 R78 sing 316 n n 
C28 N7 R78 sing 317 n n 
N7 C30 R78 sing 318 n n 
C18 C19 R78 doub 319 n y 
C16 O3 R78 sing 320 n n 
O3 C31 R78 sing 321 n n 
N5 C1 R78 sing 322 n n 
C1 N2 R78 doub 323 n y 
N2 C2 R78 sing 324 n y 
C2 C3 R78 doub 325 n y 
N4 C11 R78 sing 326 n n 
N4 C3 R78 sing 327 n n 
C4 H4 R78 sing 328 n n 
C5 H5 R78 sing 329 n n 
C8 H8 R78 sing 330 n n 
C10 H10 R78 sing 331 n n 
C10 H10A R78 sing 332 n n 
C10 H10B R78 sing 333 n n 
C13 H13 R78 sing 334 n n 
C13 H13A R78 sing 335 n n 
C15 H15 R78 sing 336 n n 
C15 H15A R78 sing 337 n n 
C17 H17 R78 sing 338 n n 
C20 H20 R78 sing 339 n n 
C22 H22 R78 sing 340 n n 
C24 H24 R78 sing 341 n n 
C24 H24A R78 sing 342 n n 
C28 H28 R78 sing 343 n n 
C28 H28A R78 sing 344 n n 
N6 HN6 R78 sing 345 n n 
C29 H29 R78 sing 346 n n 
C29 H29A R78 sing 347 n n 
C30 H30 R78 sing 348 n n 
C30 H30A R78 sing 349 n n 
C30 H30B R78 sing 350 n n 
C23 H23 R78 sing 351 n n 
C23 H23A R78 sing 352 n n 
C31 H31 R78 sing 353 n n 
C31 H31A R78 sing 354 n n 
C31 H31B R78 sing 355 n n 
C19 H19 R78 sing 356 n n 
N5 HN5 R78 sing 357 n n 
C14 H14 R78 sing 358 n n 
C14 H14A R78 sing 359 n n 
C12 H12 R78 sing 360 n n 
C12 H12A R78 sing 361 n n 
C9 H9 R78 sing 362 n n 
C9 H9A R78 sing 363 n n 
C11 H11 R78 sing 364 n n 
C11 H11A R78 sing 365 n n 
C11 H11B R78 sing 366 n n 
#
_atom_sites.entry_id                     4PY6 
_atom_sites.fract_transf_matrix[1][1]    0.013455 
_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]    0.011867 
_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]    0.004551 
_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 R78 A 1 1401 4 R78 DRG . 
F 3 EDO A 1 1402 3 EDO EDO . 
G 2 R78 B 1 1401 1 R78 DRG . 
H 3 EDO B 1 1402 1 EDO EDO . 
I 3 EDO B 1 1403 2 EDO EDO . 
J 2 R78 C 1 1401 2 R78 DRG . 
K 2 R78 D 1 1401 3 R78 DRG . 
L 4 HOH A 1 1501 1 HOH HOH . 
L 4 HOH A 2 1502 3 HOH HOH . 
L 4 HOH A 3 1503 4 HOH HOH . 
L 4 HOH A 4 1504 5 HOH HOH . 
L 4 HOH A 5 1505 6 HOH HOH . 
L 4 HOH A 6 1506 10 HOH HOH . 
L 4 HOH A 7 1507 11 HOH HOH . 
L 4 HOH A 8 1508 12 HOH HOH . 
L 4 HOH A 9 1509 13 HOH HOH . 
L 4 HOH A 10 1510 17 HOH HOH . 
L 4 HOH A 11 1511 21 HOH HOH . 
L 4 HOH A 12 1512 25 HOH HOH . 
L 4 HOH A 13 1513 26 HOH HOH . 
L 4 HOH A 14 1514 27 HOH HOH . 
L 4 HOH A 15 1515 30 HOH HOH . 
L 4 HOH A 16 1516 32 HOH HOH . 
L 4 HOH A 17 1517 33 HOH HOH . 
L 4 HOH A 18 1518 43 HOH HOH . 
L 4 HOH A 19 1519 60 HOH HOH . 
L 4 HOH A 20 1520 65 HOH HOH . 
L 4 HOH A 21 1521 67 HOH HOH . 
L 4 HOH A 22 1522 69 HOH HOH . 
L 4 HOH A 23 1523 75 HOH HOH . 
L 4 HOH A 24 1524 78 HOH HOH . 
L 4 HOH A 25 1525 79 HOH HOH . 
L 4 HOH A 26 1526 83 HOH HOH . 
L 4 HOH A 27 1527 84 HOH HOH . 
L 4 HOH A 28 1528 86 HOH HOH . 
L 4 HOH A 29 1529 87 HOH HOH . 
L 4 HOH A 30 1530 88 HOH HOH . 
L 4 HOH A 31 1531 108 HOH HOH . 
L 4 HOH A 32 1532 117 HOH HOH . 
L 4 HOH A 33 1533 119 HOH HOH . 
L 4 HOH A 34 1534 124 HOH HOH . 
L 4 HOH A 35 1535 126 HOH HOH . 
L 4 HOH A 36 1536 128 HOH HOH . 
L 4 HOH A 37 1537 130 HOH HOH . 
L 4 HOH A 38 1538 135 HOH HOH . 
L 4 HOH A 39 1539 142 HOH HOH . 
L 4 HOH A 40 1540 144 HOH HOH . 
L 4 HOH A 41 1541 146 HOH HOH . 
L 4 HOH A 42 1542 154 HOH HOH . 
L 4 HOH A 43 1543 155 HOH HOH . 
L 4 HOH A 44 1544 157 HOH HOH . 
L 4 HOH A 45 1545 158 HOH HOH . 
L 4 HOH A 46 1546 161 HOH HOH . 
M 4 HOH B 1 1501 15 HOH HOH . 
M 4 HOH B 2 1502 16 HOH HOH . 
M 4 HOH B 3 1503 29 HOH HOH . 
M 4 HOH B 4 1504 40 HOH HOH . 
M 4 HOH B 5 1505 44 HOH HOH . 
M 4 HOH B 6 1506 45 HOH HOH . 
M 4 HOH B 7 1507 46 HOH HOH . 
M 4 HOH B 8 1508 51 HOH HOH . 
M 4 HOH B 9 1509 58 HOH HOH . 
M 4 HOH B 10 1510 68 HOH HOH . 
M 4 HOH B 11 1511 70 HOH HOH . 
M 4 HOH B 12 1512 71 HOH HOH . 
M 4 HOH B 13 1513 72 HOH HOH . 
M 4 HOH B 14 1514 73 HOH HOH . 
M 4 HOH B 15 1515 76 HOH HOH . 
M 4 HOH B 16 1516 77 HOH HOH . 
M 4 HOH B 17 1517 80 HOH HOH . 
M 4 HOH B 18 1518 81 HOH HOH . 
M 4 HOH B 19 1519 82 HOH HOH . 
M 4 HOH B 20 1520 90 HOH HOH . 
M 4 HOH B 21 1521 92 HOH HOH . 
M 4 HOH B 22 1522 93 HOH HOH . 
M 4 HOH B 23 1523 94 HOH HOH . 
M 4 HOH B 24 1524 95 HOH HOH . 
M 4 HOH B 25 1525 96 HOH HOH . 
M 4 HOH B 26 1526 97 HOH HOH . 
M 4 HOH B 27 1527 98 HOH HOH . 
M 4 HOH B 28 1528 99 HOH HOH . 
M 4 HOH B 29 1529 109 HOH HOH . 
M 4 HOH B 30 1530 116 HOH HOH . 
M 4 HOH B 31 1531 118 HOH HOH . 
M 4 HOH B 32 1532 134 HOH HOH . 
M 4 HOH B 33 1533 136 HOH HOH . 
M 4 HOH B 34 1534 143 HOH HOH . 
M 4 HOH B 35 1535 147 HOH HOH . 
M 4 HOH B 36 1536 148 HOH HOH . 
M 4 HOH B 37 1537 156 HOH HOH . 
M 4 HOH B 38 1538 159 HOH HOH . 
M 4 HOH B 39 1539 162 HOH HOH . 
M 4 HOH B 40 1540 163 HOH HOH . 
N 4 HOH C 1 1501 18 HOH HOH . 
N 4 HOH C 2 1502 53 HOH HOH . 
N 4 HOH C 3 1503 54 HOH HOH . 
N 4 HOH C 4 1504 55 HOH HOH . 
N 4 HOH C 5 1505 61 HOH HOH . 
N 4 HOH C 6 1506 62 HOH HOH . 
N 4 HOH C 7 1507 63 HOH HOH . 
N 4 HOH C 8 1508 64 HOH HOH . 
N 4 HOH C 9 1509 85 HOH HOH . 
N 4 HOH C 10 1510 100 HOH HOH . 
N 4 HOH C 11 1511 101 HOH HOH . 
N 4 HOH C 12 1512 102 HOH HOH . 
N 4 HOH C 13 1513 103 HOH HOH . 
N 4 HOH C 14 1514 112 HOH HOH . 
N 4 HOH C 15 1515 113 HOH HOH . 
N 4 HOH C 16 1516 115 HOH HOH . 
N 4 HOH C 17 1517 120 HOH HOH . 
N 4 HOH C 18 1518 121 HOH HOH . 
N 4 HOH C 19 1519 122 HOH HOH . 
N 4 HOH C 20 1520 125 HOH HOH . 
N 4 HOH C 21 1521 129 HOH HOH . 
N 4 HOH C 22 1522 140 HOH HOH . 
N 4 HOH C 23 1523 141 HOH HOH . 
N 4 HOH C 24 1524 149 HOH HOH . 
N 4 HOH C 25 1525 150 HOH HOH . 
N 4 HOH C 26 1526 151 HOH HOH . 
N 4 HOH C 27 1527 152 HOH HOH . 
N 4 HOH C 28 1528 153 HOH HOH . 
O 4 HOH D 1 1501 2 HOH HOH . 
O 4 HOH D 2 1502 48 HOH HOH . 
O 4 HOH D 3 1503 50 HOH HOH . 
O 4 HOH D 4 1504 57 HOH HOH . 
O 4 HOH D 5 1505 59 HOH HOH . 
O 4 HOH D 6 1506 104 HOH HOH . 
O 4 HOH D 7 1507 105 HOH HOH . 
O 4 HOH D 8 1508 106 HOH HOH . 
O 4 HOH D 9 1509 107 HOH HOH . 
O 4 HOH D 10 1510 110 HOH HOH . 
O 4 HOH D 11 1511 111 HOH HOH . 
O 4 HOH D 12 1512 114 HOH HOH . 
O 4 HOH D 13 1513 123 HOH HOH . 
O 4 HOH D 14 1514 131 HOH HOH . 
O 4 HOH D 15 1515 132 HOH HOH . 
O 4 HOH D 16 1516 137 HOH HOH . 
O 4 HOH D 17 1517 138 HOH HOH . 
O 4 HOH D 18 1518 139 HOH HOH . 
O 4 HOH D 19 1519 145 HOH HOH . 
O 4 HOH D 20 1520 160 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 R78 . . . J 2 -15.54 -22.5 -14.673 1 79.86 ? N1 R78 1401 C 1 
HETATM 2 N N3 R78 . . . J 2 -18.529 -19.794 -15.482 1 76.91 ? N3 R78 1401 C 1 
HETATM 3 C C4 R78 . . . J 2 -16.876 -22.956 -14.732 1 76.01 ? C4 R78 1401 C 1 
HETATM 4 C C5 R78 . . . J 2 -19.951 -20.124 -15.079 1 73.76 ? C5 R78 1401 C 1 
HETATM 5 C C6 R78 . . . J 2 -20.228 -21.51 -15.064 1 70.8 ? C6 R78 1401 C 1 
HETATM 6 C C7 R78 . . . J 2 -12.97 -21.081 -15.527 1 87.61 ? C7 R78 1401 C 1 
HETATM 7 C C8 R78 . . . J 2 -18.164 -18.529 -16.23 1 78.93 ? C8 R78 1401 C 1 
HETATM 8 C C10 R78 . . . J 2 -19.624 -19.59 -12.588 1 78.11 ? C10 R78 1401 C 1 
HETATM 9 C C13 R78 . . . J 2 -19.135 -16.656 -17.147 1 79.11 ? C13 R78 1401 C 1 
HETATM 10 C C15 R78 . . . J 2 -17.953 -17.323 -15.336 1 81.96 ? C15 R78 1401 C 1 
HETATM 11 C C17 R78 . . . J 2 -11.199 -20.364 -17.033 1 90.88 ? C17 R78 1401 C 1 
HETATM 12 C C20 R78 . . . J 2 -12.352 -22.332 -15.385 1 87.36 ? C20 R78 1401 C 1 
HETATM 13 C C21 R78 . . . J 2 -9.463 -21.91 -17.657 1 91.55 ? C21 R78 1401 C 1 
HETATM 14 C C18 R78 . . . J 2 -10.617 -21.632 -16.935 1 90.43 ? C18 R78 1401 C 1 
HETATM 15 C C16 R78 . . . J 2 -12.343 -20.069 -16.28 1 89.58 ? C16 R78 1401 C 1 
HETATM 16 O O3 R78 . . . J 2 -12.963 -18.846 -16.355 1 89.8 ? O3 R78 1401 C 1 
HETATM 17 C C31 R78 . . . J 2 -12.353 -17.827 -15.539 1 93.72 ? C31 R78 1401 C 1 
HETATM 18 C C19 R78 . . . J 2 -11.193 -22.615 -16.119 1 88.65 ? C19 R78 1401 C 1 
HETATM 19 N N5 R78 . . . J 2 -14.02 -20.714 -14.783 1 86.55 ? N5 R78 1401 C 1 
HETATM 20 C C1 R78 . . . J 2 -15.254 -21.208 -14.941 1 82.58 ? C1 R78 1401 C 1 
HETATM 21 N N2 R78 . . . J 2 -16.261 -20.332 -15.14 1 81.61 ? N2 R78 1401 C 1 
HETATM 22 C C2 R78 . . . J 2 -17.561 -20.707 -15.222 1 77.8 ? C2 R78 1401 C 1 
HETATM 23 C C14 R78 . . . J 2 -18.452 -16.25 -16.072 1 82.02 ? C14 R78 1401 C 1 
HETATM 24 C C12 R78 . . . J 2 -19.176 -18.047 -17.25 1 76.79 ? C12 R78 1401 C 1 
HETATM 25 C C9 R78 . . . J 2 -20.501 -19.389 -13.829 1 75.31 ? C9 R78 1401 C 1 
HETATM 26 O O1 R78 . . . J 2 -21.403 -21.883 -15.127 1 67.91 ? O1 R78 1401 C 1 
HETATM 27 N N4 R78 . . . J 2 -19.223 -22.432 -15.059 1 71.18 ? N4 R78 1401 C 1 
HETATM 28 C C11 R78 . . . J 2 -19.59 -23.884 -15.072 1 67.98 ? C11 R78 1401 C 1 
HETATM 29 C C3 R78 . . . J 2 -17.913 -22.052 -15.012 1 74.86 ? C3 R78 1401 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           29 
#