data_4IKT # _model_server_result.job_id 2ufRWi9pfQWKhc0K2cUOXg _model_server_result.datetime_utc '2024-12-26 12:08:15' _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 4ikt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4IKT # _exptl.entry_id 4IKT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 408.808 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[5-(trifluoromethyl)pyridin-2-yl]ethane-1,2-diamine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.73 _cell.angle_gamma 90 _cell.entry_id 4IKT _cell.length_a 47.185 _cell.length_b 77.372 _cell.length_c 47.69 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IKT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A O SER 141 A SER 205 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc2 A O ASN 143 A ASN 207 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc3 A O VAL 145 A VAL 209 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc4 A NE2 HIS 148 A HIS 212 1_555 E CO CO . A CO 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc5 A OD1 ASP 165 A ASP 229 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc6 A OD2 ASP 165 A ASP 229 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 A OD2 ASP 176 A ASP 240 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc8 A OD1 ASP 176 A ASP 240 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc9 A NE2 HIS 239 A HIS 303 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc10 A OE1 GLU 272 A GLU 336 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 A O SER 299 A SER 363 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc12 A OE2 GLU 303 A GLU 367 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc13 A OE1 GLU 303 A GLU 367 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc14 B N2 TFV . A TFV 401 1_555 E CO CO . A CO 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc15 B N1 TFV . A TFV 401 1_555 E CO CO . A CO 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc16 C CO CO . A CO 402 1_555 H O HOH . A HOH 580 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc17 D CO CO . A CO 403 1_555 H O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc18 D CO CO . A CO 403 1_555 H O HOH . A HOH 580 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc19 E CO CO . A CO 404 1_555 H O HOH . A HOH 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc20 E CO CO . A CO 404 1_555 H O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc21 E CO CO . A CO 404 1_555 H O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc22 F K K . A K 405 1_555 H O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? # _chem_comp.formula 'C18 H16 Cl F3 N6' _chem_comp.formula_weight 408.808 _chem_comp.id TFV _chem_comp.mon_nstd_flag . _chem_comp.name "N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[5-(trifluoromethyl)pyridin-2-yl]ethane-1,2-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 C1 C2 TFV doub 303 n y C1 N1 TFV sing 304 n y C2 C3 TFV sing 305 n y N1 C5 TFV doub 306 n y C3 C4 TFV doub 307 n y C5 C4 TFV sing 308 n y C5 C6 TFV sing 309 n n N2 C6 TFV doub 310 n y N2 C9 TFV sing 311 n y C6 N3 TFV sing 312 n y C12 C9 TFV sing 313 n n C9 C8 TFV doub 314 n y N3 C7 TFV doub 315 n y C8 C7 TFV sing 316 n y C8 CL TFV sing 317 n n C7 N4 TFV sing 318 n n N4 C10 TFV sing 319 n n C10 C11 TFV sing 320 n n C11 N5 TFV sing 321 n n N6 C14 TFV doub 322 n y N6 C13 TFV sing 323 n y N5 C13 TFV sing 324 n n C14 C15 TFV sing 325 n y F2 C18 TFV sing 326 n n C13 C17 TFV doub 327 n y C15 C18 TFV sing 328 n n C15 C16 TFV doub 329 n y C17 C16 TFV sing 330 n y C18 F1 TFV sing 331 n n C18 F3 TFV sing 332 n n C14 H1 TFV sing 333 n n C16 H2 TFV sing 334 n n C17 H3 TFV sing 335 n n N5 H4 TFV sing 336 n n C11 H5 TFV sing 337 n n C11 H6 TFV sing 338 n n C10 H7 TFV sing 339 n n C10 H8 TFV sing 340 n n N4 H9 TFV sing 341 n n C12 H10 TFV sing 342 n n C12 H11 TFV sing 343 n n C12 H12 TFV sing 344 n n C4 H13 TFV sing 345 n n C3 H14 TFV sing 346 n n C2 H15 TFV sing 347 n n C1 H16 TFV sing 348 n n # _atom_sites.entry_id 4IKT _atom_sites.fract_transf_matrix[1][1] 0.021193 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00064 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012925 _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] 0.020978 _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 B 2 TFV A 1 401 410 TFV PTF . C 3 CO A 1 402 401 CO CO . D 3 CO A 1 403 402 CO CO . E 3 CO A 1 404 81 CO CO . F 4 K A 1 405 404 K K . G 5 GOL A 1 406 470 GOL GOL . H 6 HOH A 1 501 1 HOH HOH . H 6 HOH A 2 502 2 HOH HOH . H 6 HOH A 3 503 3 HOH HOH . H 6 HOH A 4 504 4 HOH HOH . H 6 HOH A 5 505 5 HOH HOH . H 6 HOH A 6 506 6 HOH HOH . H 6 HOH A 7 507 7 HOH HOH . H 6 HOH A 8 508 8 HOH HOH . H 6 HOH A 9 509 9 HOH HOH . H 6 HOH A 10 510 10 HOH HOH . H 6 HOH A 11 511 11 HOH HOH . H 6 HOH A 12 512 12 HOH HOH . H 6 HOH A 13 513 13 HOH HOH . H 6 HOH A 14 514 14 HOH HOH . H 6 HOH A 15 515 15 HOH HOH . H 6 HOH A 16 516 16 HOH HOH . H 6 HOH A 17 517 17 HOH HOH . H 6 HOH A 18 518 18 HOH HOH . H 6 HOH A 19 519 19 HOH HOH . H 6 HOH A 20 520 20 HOH HOH . H 6 HOH A 21 521 21 HOH HOH . H 6 HOH A 22 522 22 HOH HOH . H 6 HOH A 23 523 23 HOH HOH . H 6 HOH A 24 524 24 HOH HOH . H 6 HOH A 25 525 25 HOH HOH . H 6 HOH A 26 526 26 HOH HOH . H 6 HOH A 27 527 27 HOH HOH . H 6 HOH A 28 528 28 HOH HOH . H 6 HOH A 29 529 29 HOH HOH . H 6 HOH A 30 530 30 HOH HOH . H 6 HOH A 31 531 31 HOH HOH . H 6 HOH A 32 532 32 HOH HOH . H 6 HOH A 33 533 33 HOH HOH . H 6 HOH A 34 534 34 HOH HOH . H 6 HOH A 35 535 35 HOH HOH . H 6 HOH A 36 536 37 HOH HOH . H 6 HOH A 37 537 38 HOH HOH . H 6 HOH A 38 538 39 HOH HOH . H 6 HOH A 39 539 40 HOH HOH . H 6 HOH A 40 540 41 HOH HOH . H 6 HOH A 41 541 42 HOH HOH . H 6 HOH A 42 542 43 HOH HOH . H 6 HOH A 43 543 44 HOH HOH . H 6 HOH A 44 544 45 HOH HOH . H 6 HOH A 45 545 46 HOH HOH . H 6 HOH A 46 546 47 HOH HOH . H 6 HOH A 47 547 48 HOH HOH . H 6 HOH A 48 548 49 HOH HOH . H 6 HOH A 49 549 50 HOH HOH . H 6 HOH A 50 550 51 HOH HOH . H 6 HOH A 51 551 52 HOH HOH . H 6 HOH A 52 552 53 HOH HOH . H 6 HOH A 53 553 54 HOH HOH . H 6 HOH A 54 554 55 HOH HOH . H 6 HOH A 55 555 56 HOH HOH . H 6 HOH A 56 556 57 HOH HOH . H 6 HOH A 57 557 58 HOH HOH . H 6 HOH A 58 558 59 HOH HOH . H 6 HOH A 59 559 60 HOH HOH . H 6 HOH A 60 560 61 HOH HOH . H 6 HOH A 61 561 62 HOH HOH . H 6 HOH A 62 562 63 HOH HOH . H 6 HOH A 63 563 64 HOH HOH . H 6 HOH A 64 564 65 HOH HOH . H 6 HOH A 65 565 66 HOH HOH . H 6 HOH A 66 566 67 HOH HOH . H 6 HOH A 67 567 68 HOH HOH . H 6 HOH A 68 568 69 HOH HOH . H 6 HOH A 69 569 70 HOH HOH . H 6 HOH A 70 570 71 HOH HOH . H 6 HOH A 71 571 73 HOH HOH . H 6 HOH A 72 572 74 HOH HOH . H 6 HOH A 73 573 75 HOH HOH . H 6 HOH A 74 574 76 HOH HOH . H 6 HOH A 75 575 77 HOH HOH . H 6 HOH A 76 576 78 HOH HOH . H 6 HOH A 77 577 82 HOH HOH . H 6 HOH A 78 578 83 HOH HOH . H 6 HOH A 79 579 84 HOH HOH . H 6 HOH A 80 580 85 HOH HOH . H 6 HOH A 81 581 87 HOH HOH . H 6 HOH A 82 582 88 HOH HOH . H 6 HOH A 83 583 89 HOH HOH . H 6 HOH A 84 584 90 HOH HOH . H 6 HOH A 85 585 91 HOH HOH . H 6 HOH A 86 586 92 HOH HOH . H 6 HOH A 87 587 93 HOH HOH . H 6 HOH A 88 588 94 HOH HOH . H 6 HOH A 89 589 95 HOH HOH . H 6 HOH A 90 590 96 HOH HOH . H 6 HOH A 91 591 97 HOH HOH . H 6 HOH A 92 592 98 HOH HOH . H 6 HOH A 93 593 99 HOH HOH . H 6 HOH A 94 594 100 HOH HOH . H 6 HOH A 95 595 101 HOH HOH . H 6 HOH A 96 596 102 HOH HOH . H 6 HOH A 97 597 103 HOH HOH . H 6 HOH A 98 598 104 HOH HOH . H 6 HOH A 99 599 105 HOH HOH . H 6 HOH A 100 600 106 HOH HOH . H 6 HOH A 101 601 107 HOH HOH . H 6 HOH A 102 602 108 HOH HOH . H 6 HOH A 103 603 109 HOH HOH . H 6 HOH A 104 604 110 HOH HOH . H 6 HOH A 105 605 111 HOH HOH . H 6 HOH A 106 606 112 HOH HOH . H 6 HOH A 107 607 113 HOH HOH . H 6 HOH A 108 608 114 HOH HOH . H 6 HOH A 109 609 115 HOH HOH . H 6 HOH A 110 610 116 HOH HOH . H 6 HOH A 111 611 121 HOH HOH . H 6 HOH A 112 612 122 HOH HOH . H 6 HOH A 113 613 123 HOH HOH . H 6 HOH A 114 614 124 HOH HOH . H 6 HOH A 115 615 125 HOH HOH . H 6 HOH A 116 616 126 HOH HOH . H 6 HOH A 117 617 127 HOH HOH . H 6 HOH A 118 618 128 HOH HOH . H 6 HOH A 119 619 129 HOH HOH . H 6 HOH A 120 620 130 HOH HOH . H 6 HOH A 121 621 131 HOH HOH . H 6 HOH A 122 622 132 HOH HOH . H 6 HOH A 123 623 133 HOH HOH . H 6 HOH A 124 624 134 HOH HOH . H 6 HOH A 125 625 135 HOH HOH . H 6 HOH A 126 626 136 HOH HOH . H 6 HOH A 127 627 137 HOH HOH . H 6 HOH A 128 628 138 HOH HOH . H 6 HOH A 129 629 139 HOH HOH . H 6 HOH A 130 630 140 HOH HOH . H 6 HOH A 131 631 141 HOH HOH . H 6 HOH A 132 632 142 HOH HOH . H 6 HOH A 133 633 143 HOH HOH . H 6 HOH A 134 634 144 HOH HOH . H 6 HOH A 135 635 145 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 F F3 TFV . . . B 2 20.501 -0.19 22.385 1 45.12 ? F3 TFV 401 A 1 HETATM 2 C C18 TFV . . . B 2 19.866 -0.718 21.362 1 43.03 ? C18 TFV 401 A 1 HETATM 3 F F1 TFV . . . B 2 18.581 -0.745 21.669 1 44.67 ? F1 TFV 401 A 1 HETATM 4 F F2 TFV . . . B 2 20.066 0.086 20.327 1 44.37 ? F2 TFV 401 A 1 HETATM 5 C C15 TFV . . . B 2 20.363 -2.112 21.048 1 41.63 ? C15 TFV 401 A 1 HETATM 6 C C14 TFV . . . B 2 19.678 -2.912 20.127 1 41.09 ? C14 TFV 401 A 1 HETATM 7 N N6 TFV . . . B 2 20.106 -4.154 19.822 1 39.95 ? N6 TFV 401 A 1 HETATM 8 C C16 TFV . . . B 2 21.524 -2.623 21.642 1 41.18 ? C16 TFV 401 A 1 HETATM 9 C C17 TFV . . . B 2 21.952 -3.918 21.312 1 40.98 ? C17 TFV 401 A 1 HETATM 10 C C13 TFV . . . B 2 21.224 -4.686 20.391 1 40.51 ? C13 TFV 401 A 1 HETATM 11 N N5 TFV . . . B 2 21.659 -5.94 20.073 1 40.7 ? N5 TFV 401 A 1 HETATM 12 C C11 TFV . . . B 2 20.878 -6.917 19.321 1 38.08 ? C11 TFV 401 A 1 HETATM 13 C C10 TFV . . . B 2 21.144 -6.882 17.812 1 35.46 ? C10 TFV 401 A 1 HETATM 14 N N4 TFV . . . B 2 20.641 -5.644 17.255 1 32.61 ? N4 TFV 401 A 1 HETATM 15 C C7 TFV . . . B 2 20.646 -5.363 15.934 1 28.33 ? C7 TFV 401 A 1 HETATM 16 N N3 TFV . . . B 2 21.21 -6.201 15.031 1 26.83 ? N3 TFV 401 A 1 HETATM 17 C C8 TFV . . . B 2 20.051 -4.181 15.507 1 26.58 ? C8 TFV 401 A 1 HETATM 18 CL CL TFV . . . B 2 19.319 -3.05 16.68 1 30.27 ? CL TFV 401 A 1 HETATM 19 C C9 TFV . . . B 2 20.03 -3.836 14.174 1 25.22 ? C9 TFV 401 A 1 HETATM 20 C C12 TFV . . . B 2 19.394 -2.545 13.727 1 22.65 ? C12 TFV 401 A 1 HETATM 21 N N2 TFV . . . B 2 20.623 -4.684 13.3 1 19.47 ? N2 TFV 401 A 1 HETATM 22 C C6 TFV . . . B 2 21.167 -5.854 13.716 1 22.82 ? C6 TFV 401 A 1 HETATM 23 C C5 TFV . . . B 2 21.843 -6.687 12.7 1 21.18 ? C5 TFV 401 A 1 HETATM 24 N N1 TFV . . . B 2 22.187 -6.045 11.556 1 19.26 ? N1 TFV 401 A 1 HETATM 25 C C4 TFV . . . B 2 22.207 -8.011 12.906 1 20.07 ? C4 TFV 401 A 1 HETATM 26 C C3 TFV . . . B 2 22.87 -8.672 11.884 1 17.47 ? C3 TFV 401 A 1 HETATM 27 C C2 TFV . . . B 2 23.21 -8 10.721 1 15.38 ? C2 TFV 401 A 1 HETATM 28 C C1 TFV . . . B 2 22.841 -6.661 10.569 1 15.76 ? C1 TFV 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #