data_7RGK
#
_model_server_result.job_id            dFkrbgb1TdhJcTgwiimY2Q 
_model_server_result.datetime_utc      '2024-11-17 23:44:47' 
_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          7rgk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":204}' 
#
_entry.id    7RGK 
#
_exptl.entry_id    7RGK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              415.488 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-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            7RGK 
_cell.length_a            99.42 
_cell.length_b            99.42 
_cell.length_c            43.406 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7RGK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    'P 4cw' 
_symmetry.space_group_name_H-M     'P 43' 
#
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 J N N 
#
_chem_comp.formula           'C24 H25 N5 O2' 
_chem_comp.formula_weight    415.488 
_chem_comp.id                560 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-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
NAE C6 560 sing 1 n n 
CAJ CAI 560 sing 2 n n 
C6 N1 560 doub 3 n y 
C6 C5 560 sing 4 n y 
N1 C2 560 sing 5 n y 
CAI CAH 560 sing 6 n n 
CAI CAK 560 sing 7 n n 
CAH CAG 560 trip 8 n n 
CAG C5 560 sing 9 n n 
C5 C4 560 doub 10 n y 
C2 NAA 560 sing 11 n n 
C2 N3 560 doub 12 n y 
CAK CAL 560 doub 13 n y 
CAK CBA 560 sing 14 n y 
CAL CAM 560 sing 15 n y 
CBA CAZ 560 doub 16 n y 
C4 N3 560 sing 17 n y 
C4 CBC 560 sing 18 n n 
CAU CAT 560 doub 19 n y 
CAU CAN 560 sing 20 n y 
CAM CAN 560 sing 21 n n 
CAM CAV 560 doub 22 n y 
CAZ CAV 560 sing 23 n y 
CAZ OAY 560 sing 24 n n 
NAS CAR 560 sing 25 n n 
CAT CAQ 560 sing 26 n y 
CAN CAO 560 doub 27 n y 
CAV OAW 560 sing 28 n n 
OAY CAX 560 sing 29 n n 
CBC CBD 560 sing 30 n n 
CAQ CAR 560 sing 31 n n 
CAQ CAP 560 doub 32 n y 
CAO CAP 560 sing 33 n y 
OAW CAX 560 sing 34 n n 
CAI H1 560 sing 35 n n 
CAJ H2 560 sing 36 n n 
CAJ H3 560 sing 37 n n 
CAJ H4 560 sing 38 n n 
CAL H5 560 sing 39 n n 
CAO H6 560 sing 40 n n 
CAP H7 560 sing 41 n n 
CAR H8 560 sing 42 n n 
CAR H9 560 sing 43 n n 
CAT H10 560 sing 44 n n 
CAU H11 560 sing 45 n n 
CAX H12 560 sing 46 n n 
CAX H13 560 sing 47 n n 
CBA H14 560 sing 48 n n 
CBC H15 560 sing 49 n n 
CBC H16 560 sing 50 n n 
CBD H17 560 sing 51 n n 
CBD H18 560 sing 52 n n 
CBD H19 560 sing 53 n n 
NAA H20 560 sing 54 n n 
NAA H21 560 sing 55 n n 
NAE H22 560 sing 56 n n 
NAE H23 560 sing 57 n n 
NAS H24 560 sing 58 n n 
NAS H25 560 sing 59 n n 
#
_atom_sites.entry_id                     7RGK 
_atom_sites.fract_transf_matrix[1][1]    0.010058 
_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]    0.010058 
_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]    0.023038 
_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 NAP A 1 201 201 NAP NAP . 
D 3 SO4 A 1 202 2 SO4 SO4 . 
E 3 SO4 A 1 203 3 SO4 SO4 . 
F 4 560 A 1 204 1 560 DRG . 
G 2 NAP B 1 201 202 NAP NAP . 
H 3 SO4 B 1 202 1 SO4 SO4 . 
I 3 SO4 B 1 203 4 SO4 SO4 . 
J 4 560 B 1 204 2 560 DRG . 
K 5 HOH A 1 301 25 HOH HOH . 
K 5 HOH A 2 302 17 HOH HOH . 
K 5 HOH A 3 303 8 HOH HOH . 
K 5 HOH A 4 304 5 HOH HOH . 
K 5 HOH A 5 305 46 HOH HOH . 
K 5 HOH A 6 306 1 HOH HOH . 
K 5 HOH A 7 307 29 HOH HOH . 
K 5 HOH A 8 308 35 HOH HOH . 
K 5 HOH A 9 309 33 HOH HOH . 
K 5 HOH A 10 310 36 HOH HOH . 
K 5 HOH A 11 311 3 HOH HOH . 
K 5 HOH A 12 312 39 HOH HOH . 
K 5 HOH A 13 313 47 HOH HOH . 
K 5 HOH A 14 314 13 HOH HOH . 
K 5 HOH A 15 315 4 HOH HOH . 
K 5 HOH A 16 316 18 HOH HOH . 
K 5 HOH A 17 317 28 HOH HOH . 
K 5 HOH A 18 318 41 HOH HOH . 
K 5 HOH A 19 319 40 HOH HOH . 
L 5 HOH B 1 301 20 HOH HOH . 
L 5 HOH B 2 302 27 HOH HOH . 
L 5 HOH B 3 303 22 HOH HOH . 
L 5 HOH B 4 304 19 HOH HOH . 
L 5 HOH B 5 305 14 HOH HOH . 
L 5 HOH B 6 306 32 HOH HOH . 
L 5 HOH B 7 307 15 HOH HOH . 
L 5 HOH B 8 308 26 HOH HOH . 
L 5 HOH B 9 309 2 HOH HOH . 
L 5 HOH B 10 310 7 HOH HOH . 
L 5 HOH B 11 311 38 HOH HOH . 
L 5 HOH B 12 312 6 HOH HOH . 
L 5 HOH B 13 313 37 HOH HOH . 
L 5 HOH B 14 314 10 HOH HOH . 
L 5 HOH B 15 315 23 HOH HOH . 
L 5 HOH B 16 316 30 HOH HOH . 
L 5 HOH B 17 317 12 HOH HOH . 
L 5 HOH B 18 318 21 HOH HOH . 
L 5 HOH B 19 319 16 HOH HOH . 
L 5 HOH B 20 320 9 HOH HOH . 
L 5 HOH B 21 321 45 HOH HOH . 
L 5 HOH B 22 322 24 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 560 . A . J 4 111.664 45.116 10.238 0.52 54.29 ? C4 560 204 B 1 
HETATM 2 C C4 560 . B . J 4 111.678 45.08 9.713 0.48 53.88 ? C4 560 204 B 1 
HETATM 3 C C5 560 . A . J 4 111.409 44.635 8.967 0.52 53.77 ? C5 560 204 B 1 
HETATM 4 C C5 560 . B . J 4 111.479 44.912 8.353 0.48 55.51 ? C5 560 204 B 1 
HETATM 5 C C6 560 . A . J 4 112.318 44.912 7.962 0.52 51.53 ? C6 560 204 B 1 
HETATM 6 C C6 560 . B . J 4 112.491 45.321 7.495 0.48 51.89 ? C6 560 204 B 1 
HETATM 7 N N1 560 . A . J 4 113.414 45.634 8.219 0.52 49.52 ? N1 560 204 B 1 
HETATM 8 N N1 560 . B . J 4 113.614 45.866 7.978 0.48 52.68 ? N1 560 204 B 1 
HETATM 9 N N3 560 . A . J 4 112.779 45.833 10.456 0.52 51.79 ? N3 560 204 B 1 
HETATM 10 N N3 560 . B . J 4 112.823 45.626 10.157 0.48 52.45 ? N3 560 204 B 1 
HETATM 11 C C2 560 . A . J 4 113.645 46.088 9.459 0.52 48.87 ? C2 560 204 B 1 
HETATM 12 C C2 560 . B . J 4 113.782 46.015 9.298 0.48 50.71 ? C2 560 204 B 1 
HETATM 13 C CAG 560 . A . J 4 110.257 43.891 8.716 0.52 59.3 ? CAG 560 204 B 1 
HETATM 14 C CAG 560 . B . J 4 110.247 44.325 7.86 0.48 60.28 ? CAG 560 204 B 1 
HETATM 15 C CAH 560 . A . J 4 109.415 43.361 8.548 0.52 64.42 ? CAH 560 204 B 1 
HETATM 16 C CAH 560 . B . J 4 109.196 43.818 7.404 0.48 62.1 ? CAH 560 204 B 1 
HETATM 17 C CAI 560 . A . J 4 108.15 42.538 8.327 0.52 67.75 ? CAI 560 204 B 1 
HETATM 18 C CAI 560 . B . J 4 108.008 43.23 6.787 0.48 66.72 ? CAI 560 204 B 1 
HETATM 19 C CAJ 560 . A . J 4 107.598 42.557 6.874 0.52 69.17 ? CAJ 560 204 B 1 
HETATM 20 C CAJ 560 . B . J 4 108.224 43.318 5.306 0.48 72.23 ? CAJ 560 204 B 1 
HETATM 21 C CAK 560 . A . J 4 107.097 42.641 9.243 0.52 75.42 ? CAK 560 204 B 1 
HETATM 22 C CAK 560 . B . J 4 106.919 43.997 6.981 0.48 73.35 ? CAK 560 204 B 1 
HETATM 23 C CAL 560 . A . J 4 106.551 43.716 9.954 0.52 81.06 ? CAL 560 204 B 1 
HETATM 24 C CAL 560 . B . J 4 106.689 44.596 8.195 0.48 76.12 ? CAL 560 204 B 1 
HETATM 25 C CAM 560 . A . J 4 105.465 43.422 10.808 0.52 87.2 ? CAM 560 204 B 1 
HETATM 26 C CAM 560 . B . J 4 105.555 45.361 8.284 0.48 82.19 ? CAM 560 204 B 1 
HETATM 27 C CAN 560 . A . J 4 104.854 44.415 11.61 0.52 93.42 ? CAN 560 204 B 1 
HETATM 28 C CAN 560 . B . J 4 105.249 46 9.463 0.48 86.54 ? CAN 560 204 B 1 
HETATM 29 C CAO 560 . A . J 4 103.921 44.018 12.56 0.52 95.04 ? CAO 560 204 B 1 
HETATM 30 C CAO 560 . B . J 4 106.222 46.763 10.083 0.48 86.04 ? CAO 560 204 B 1 
HETATM 31 C CAP 560 . A . J 4 103.274 44.862 13.424 0.52 101.44 ? CAP 560 204 B 1 
HETATM 32 C CAP 560 . B . J 4 105.903 47.414 11.26 0.48 95.11 ? CAP 560 204 B 1 
HETATM 33 C CAQ 560 . A . J 4 103.616 46.18 13.328 0.52 107.73 ? CAQ 560 204 B 1 
HETATM 34 C CAQ 560 . B . J 4 104.639 47.277 11.797 0.48 101.67 ? CAQ 560 204 B 1 
HETATM 35 C CAR 560 . A . J 4 102.984 47.042 14.152 0.52 112.5 ? CAR 560 204 B 1 
HETATM 36 C CAR 560 . B . J 4 104.317 47.913 12.965 0.48 110.19 ? CAR 560 204 B 1 
HETATM 37 C CAT 560 . A . J 4 104.546 46.65 12.402 0.52 103.39 ? CAT 560 204 B 1 
HETATM 38 C CAT 560 . B . J 4 103.661 46.519 11.192 0.48 96.45 ? CAT 560 204 B 1 
HETATM 39 C CAU 560 . A . J 4 105.194 45.764 11.539 0.52 98.7 ? CAU 560 204 B 1 
HETATM 40 C CAU 560 . B . J 4 103.981 45.871 10.013 0.48 90.1 ? CAU 560 204 B 1 
HETATM 41 C CAV 560 . A . J 4 105.003 42.146 10.933 0.52 89.21 ? CAV 560 204 B 1 
HETATM 42 C CAV 560 . B . J 4 104.73 45.54 7.237 0.48 87.63 ? CAV 560 204 B 1 
HETATM 43 C CAX 560 . A . J 4 104.31 40.199 11.69 0.52 84.26 ? CAX 560 204 B 1 
HETATM 44 C CAX 560 . B . J 4 103.357 46.366 5.78 0.48 78.12 ? CAX 560 204 B 1 
HETATM 45 C CAZ 560 . A . J 4 105.558 41.168 10.221 0.52 82.89 ? CAZ 560 204 B 1 
HETATM 46 C CAZ 560 . B . J 4 104.972 44.947 6.071 0.48 80.15 ? CAZ 560 204 B 1 
HETATM 47 C CBA 560 . A . J 4 106.55 41.406 9.415 0.52 79.12 ? CBA 560 204 B 1 
HETATM 48 C CBA 560 . B . J 4 106.03 44.186 5.928 0.48 76.75 ? CBA 560 204 B 1 
HETATM 49 C CBC 560 . A . J 4 110.772 44.852 11.278 0.52 56.37 ? CBC 560 204 B 1 
HETATM 50 C CBC 560 . B . J 4 110.685 44.677 10.601 0.48 57.2 ? CBC 560 204 B 1 
HETATM 51 C CBD 560 . A . J 4 109.706 45.951 11.373 0.52 57.99 ? CBD 560 204 B 1 
HETATM 52 C CBD 560 . B . J 4 111.017 45.113 12.031 0.48 54.57 ? CBD 560 204 B 1 
HETATM 53 N NAA 560 . A . J 4 114.743 46.798 9.696 0.52 45.83 ? NAA 560 204 B 1 
HETATM 54 N NAA 560 . B . J 4 114.91 46.554 9.754 0.48 45.56 ? NAA 560 204 B 1 
HETATM 55 N NAE 560 . A . J 4 112.043 44.435 6.751 0.52 51.53 ? NAE 560 204 B 1 
HETATM 56 N NAE 560 . B . J 4 112.289 45.155 6.19 0.48 50.97 ? NAE 560 204 B 1 
HETATM 57 N NAS 560 . A . J 4 102.42 48.015 13.232 0.52 110.5 ? NAS 560 204 B 1 
HETATM 58 N NAS 560 . B . J 4 102.942 47.587 13.366 0.48 109.93 ? NAS 560 204 B 1 
HETATM 59 O OAW 560 . A . J 4 103.989 41.581 11.652 0.52 86.7 ? OAW 560 204 B 1 
HETATM 60 O OAW 560 . B . J 4 103.586 46.242 7.175 0.48 82.41 ? OAW 560 204 B 1 
HETATM 61 O OAY 560 . A . J 4 104.963 39.969 10.45 0.52 82.15 ? OAY 560 204 B 1 
HETATM 62 O OAY 560 . B . J 4 104.003 45.241 5.177 0.48 76.61 ? OAY 560 204 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           62 
#