data_4NFJ # _model_server_result.job_id C82f3uzIGWOriBRHsmoNbg _model_server_result.datetime_utc '2025-01-25 15:03:37' _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 4nfj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4NFJ # _exptl.entry_id 4NFJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 400.26 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)' _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 90 _cell.angle_gamma 90 _cell.entry_id 4NFJ _cell.length_a 111.235 _cell.length_b 111.235 _cell.length_c 67.919 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NFJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 OD2 ASP 125 F ASP 103 1_555 C MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 A OD1 ASP 125 F ASP 103 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 A OD2 ASP 129 F ASP 107 1_555 C MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc4 A OD2 ASP 129 F ASP 107 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 A OD2 ASP 265 F ASP 243 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc6 B OAK JD5 . F JD5 401 1_555 C MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc7 B OAL JD5 . F JD5 401 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc8 B OAO JD5 . F JD5 401 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc9 B OAK JD5 . F JD5 401 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc10 B OAP JD5 . F JD5 401 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc11 C MG MG . F MG 402 1_555 G O HOH . F HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc12 C MG MG . F MG 402 1_555 G O HOH . F HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc13 C MG MG . F MG 402 1_555 G O HOH . F HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc14 D MG MG . F MG 403 1_555 G O HOH . F HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc15 D MG MG . F MG 403 1_555 G O HOH . F HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc16 D MG MG . F MG 403 1_555 G O HOH . F HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc17 E MG MG . F MG 404 1_555 G O HOH . F HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc18 E MG MG . F MG 404 1_555 G O HOH . F HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? # _chem_comp.formula 'C15 H18 N2 O7 P2' _chem_comp.formula_weight 400.26 _chem_comp.id JD5 _chem_comp.mon_nstd_flag . _chem_comp.name '[({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)' _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 OAJ PAI JD5 doub 173 n n OAL PAI JD5 sing 174 n n PAI OAK JD5 sing 175 n n PAI CAH JD5 sing 176 n n NAB CAC JD5 doub 177 n y NAB CAA JD5 sing 178 n y CAC CAD JD5 sing 179 n y CAA CAF JD5 doub 180 n y CAH NAG JD5 sing 181 n n CAH PAM JD5 sing 182 n n OAO PAM JD5 doub 183 n n CAD NAG JD5 sing 184 n n CAD CAE JD5 doub 185 n y CAF CAE JD5 sing 186 n y CAF CAQ JD5 sing 187 n n PAM OAP JD5 sing 188 n n PAM OAN JD5 sing 189 n n CAQ CAV JD5 doub 190 n y CAQ CAR JD5 sing 191 n y CAV CAU JD5 sing 192 n y CAR CAS JD5 doub 193 n y CAU CAT JD5 doub 194 n y CAS CAT JD5 sing 195 n y CAT OAW JD5 sing 196 n n OAW CAX JD5 sing 197 n n CAY CAX JD5 sing 198 n n CAY CAZ JD5 sing 199 n n CAX CAZ JD5 sing 200 n n OAK H1 JD5 sing 201 n n OAL H2 JD5 sing 202 n n CAH H3 JD5 sing 203 n n OAP H4 JD5 sing 204 n n OAN H5 JD5 sing 205 n n NAG H6 JD5 sing 206 n n CAE H7 JD5 sing 207 n n CAC H8 JD5 sing 208 n n CAA H9 JD5 sing 209 n n CAV H10 JD5 sing 210 n n CAU H11 JD5 sing 211 n n CAR H12 JD5 sing 212 n n CAS H13 JD5 sing 213 n n CAX H14 JD5 sing 214 n n CAY H15 JD5 sing 215 n n CAY H16 JD5 sing 216 n n CAZ H17 JD5 sing 217 n n CAZ H18 JD5 sing 218 n n # _atom_sites.entry_id 4NFJ _atom_sites.fract_transf_matrix[1][1] 0.00899 _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] 0.00899 _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] 0.014723 _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 JD5 F 1 401 1 JD5 JD5 . C 3 MG F 1 402 1 MG MG . D 3 MG F 1 403 1 MG MG . E 3 MG F 1 404 1 MG MG . F 4 SO4 F 1 405 1 SO4 SO4 . G 5 HOH F 1 501 1 HOH HOH . G 5 HOH F 2 502 2 HOH HOH . G 5 HOH F 3 503 3 HOH HOH . G 5 HOH F 4 504 4 HOH HOH . G 5 HOH F 5 505 5 HOH HOH . G 5 HOH F 6 506 6 HOH HOH . G 5 HOH F 7 507 7 HOH HOH . G 5 HOH F 8 508 8 HOH HOH . G 5 HOH F 9 509 9 HOH HOH . G 5 HOH F 10 510 10 HOH HOH . G 5 HOH F 11 511 11 HOH HOH . G 5 HOH F 12 512 12 HOH HOH . G 5 HOH F 13 513 13 HOH HOH . G 5 HOH F 14 514 14 HOH HOH . G 5 HOH F 15 515 15 HOH HOH . G 5 HOH F 16 516 16 HOH HOH . G 5 HOH F 17 517 17 HOH HOH . G 5 HOH F 18 518 18 HOH HOH . G 5 HOH F 19 519 19 HOH HOH . G 5 HOH F 20 520 20 HOH HOH . G 5 HOH F 21 521 21 HOH HOH . G 5 HOH F 22 522 22 HOH HOH . G 5 HOH F 23 523 23 HOH HOH . G 5 HOH F 24 524 24 HOH HOH . G 5 HOH F 25 525 25 HOH HOH . G 5 HOH F 26 526 26 HOH HOH . G 5 HOH F 27 527 27 HOH HOH . G 5 HOH F 28 528 28 HOH HOH . G 5 HOH F 29 529 29 HOH HOH . G 5 HOH F 30 530 30 HOH HOH . G 5 HOH F 31 531 31 HOH HOH . G 5 HOH F 32 532 32 HOH HOH . G 5 HOH F 33 533 33 HOH HOH . G 5 HOH F 34 534 34 HOH HOH . G 5 HOH F 35 535 35 HOH HOH . G 5 HOH F 36 536 36 HOH HOH . G 5 HOH F 37 537 37 HOH HOH . G 5 HOH F 38 538 38 HOH HOH . G 5 HOH F 39 539 39 HOH HOH . G 5 HOH F 40 540 40 HOH HOH . G 5 HOH F 41 541 41 HOH HOH . G 5 HOH F 42 542 42 HOH HOH . G 5 HOH F 43 543 43 HOH HOH . G 5 HOH F 44 544 44 HOH HOH . G 5 HOH F 45 545 45 HOH HOH . G 5 HOH F 46 546 46 HOH HOH . G 5 HOH F 47 547 47 HOH HOH . G 5 HOH F 48 548 48 HOH HOH . G 5 HOH F 49 549 49 HOH HOH . G 5 HOH F 50 550 50 HOH HOH . G 5 HOH F 51 551 51 HOH HOH . G 5 HOH F 52 552 52 HOH HOH . G 5 HOH F 53 553 53 HOH HOH . G 5 HOH F 54 554 54 HOH HOH . G 5 HOH F 55 555 55 HOH HOH . G 5 HOH F 56 556 56 HOH HOH . G 5 HOH F 57 557 57 HOH HOH . G 5 HOH F 58 558 58 HOH HOH . G 5 HOH F 59 559 59 HOH HOH . G 5 HOH F 60 560 60 HOH HOH . G 5 HOH F 61 561 61 HOH HOH . G 5 HOH F 62 562 62 HOH HOH . G 5 HOH F 63 563 63 HOH HOH . G 5 HOH F 64 564 64 HOH HOH . G 5 HOH F 65 565 65 HOH HOH . G 5 HOH F 66 566 66 HOH HOH . G 5 HOH F 67 567 67 HOH HOH . G 5 HOH F 68 568 68 HOH HOH . G 5 HOH F 69 569 69 HOH HOH . G 5 HOH F 70 570 70 HOH HOH . G 5 HOH F 71 571 71 HOH HOH . G 5 HOH F 72 572 72 HOH HOH . G 5 HOH F 73 573 73 HOH HOH . G 5 HOH F 74 574 74 HOH HOH . G 5 HOH F 75 575 75 HOH HOH . G 5 HOH F 76 576 76 HOH HOH . G 5 HOH F 77 577 77 HOH HOH . G 5 HOH F 78 578 78 HOH HOH . G 5 HOH F 79 579 79 HOH HOH . G 5 HOH F 80 580 80 HOH HOH . G 5 HOH F 81 581 81 HOH HOH . G 5 HOH F 82 582 82 HOH HOH . G 5 HOH F 83 583 83 HOH HOH . G 5 HOH F 84 584 84 HOH HOH . G 5 HOH F 85 585 85 HOH HOH . G 5 HOH F 86 586 86 HOH HOH . G 5 HOH F 87 587 87 HOH HOH . G 5 HOH F 88 588 88 HOH HOH . G 5 HOH F 89 589 89 HOH HOH . G 5 HOH F 90 590 90 HOH HOH . G 5 HOH F 91 591 91 HOH HOH . G 5 HOH F 92 592 92 HOH HOH . G 5 HOH F 93 593 93 HOH HOH . G 5 HOH F 94 594 94 HOH HOH . G 5 HOH F 95 595 95 HOH HOH . G 5 HOH F 96 596 96 HOH HOH . G 5 HOH F 97 597 97 HOH HOH . G 5 HOH F 98 598 98 HOH HOH . G 5 HOH F 99 599 99 HOH HOH . G 5 HOH F 100 600 100 HOH HOH . G 5 HOH F 101 601 101 HOH HOH . G 5 HOH F 102 602 102 HOH HOH . G 5 HOH F 103 603 103 HOH HOH . G 5 HOH F 104 604 104 HOH HOH . G 5 HOH F 105 605 105 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 O OAJ JD5 . . . B 2 16.108 32.584 -10.772 1 42.03 ? OAJ JD5 401 F 1 HETATM 2 P PAI JD5 . . . B 2 16.236 34.015 -9.864 1 43.28 ? PAI JD5 401 F 1 HETATM 3 O OAK JD5 . . . B 2 17.664 33.998 -9.218 1 51.2 ? OAK JD5 401 F 1 HETATM 4 O OAL JD5 . . . B 2 15.953 35.288 -10.77 1 43.93 ? OAL JD5 401 F 1 HETATM 5 C CAH JD5 . . . B 2 14.975 33.909 -8.574 1 42.06 ? CAH JD5 401 F 1 HETATM 6 P PAM JD5 . . . B 2 15.085 35.432 -7.523 1 39.01 ? PAM JD5 401 F 1 HETATM 7 O OAO JD5 . . . B 2 15.009 36.688 -8.494 1 36.28 ? OAO JD5 401 F 1 HETATM 8 O OAP JD5 . . . B 2 16.463 35.567 -6.811 1 36.64 ? OAP JD5 401 F 1 HETATM 9 O OAN JD5 . . . B 2 14.109 35.296 -6.373 1 38.62 ? OAN JD5 401 F 1 HETATM 10 N NAG JD5 . . . B 2 15.252 32.783 -7.688 1 41.93 ? NAG JD5 401 F 1 HETATM 11 C CAD JD5 . . . B 2 15.012 31.539 -8.03 1 42.67 ? CAD JD5 401 F 1 HETATM 12 C CAE JD5 . . . B 2 15.814 30.58 -7.412 1 43.35 ? CAE JD5 401 F 1 HETATM 13 C CAC JD5 . . . B 2 14.037 31.158 -8.982 1 42.09 ? CAC JD5 401 F 1 HETATM 14 N NAB JD5 . . . B 2 13.93 29.801 -9.298 1 39.89 ? NAB JD5 401 F 1 HETATM 15 C CAA JD5 . . . B 2 14.735 28.829 -8.648 1 38.52 ? CAA JD5 401 F 1 HETATM 16 C CAF JD5 . . . B 2 15.688 29.2 -7.693 1 44.96 ? CAF JD5 401 F 1 HETATM 17 C CAQ JD5 . . . B 2 16.591 28.281 -7.072 1 52.11 ? CAQ JD5 401 F 1 HETATM 18 C CAV JD5 . . . B 2 17.937 28.652 -7.059 1 63.4 ? CAV JD5 401 F 1 HETATM 19 C CAU JD5 . . . B 2 18.922 27.867 -6.507 1 64.86 ? CAU JD5 401 F 1 HETATM 20 C CAR JD5 . . . B 2 16.27 27.049 -6.524 1 62.98 ? CAR JD5 401 F 1 HETATM 21 C CAS JD5 . . . B 2 17.25 26.239 -5.962 1 66.62 ? CAS JD5 401 F 1 HETATM 22 C CAT JD5 . . . B 2 18.577 26.643 -5.948 1 67.74 ? CAT JD5 401 F 1 HETATM 23 O OAW JD5 . . . B 2 19.608 25.903 -5.442 1 60.56 ? OAW JD5 401 F 1 HETATM 24 C CAX JD5 . . . B 2 19.367 25.05 -4.34 1 58.81 ? CAX JD5 401 F 1 HETATM 25 C CAY JD5 . . . B 2 18.985 23.763 -4.744 1 55.06 ? CAY JD5 401 F 1 HETATM 26 C CAZ JD5 . . . B 2 20.255 23.921 -4.132 1 50.83 ? CAZ JD5 401 F 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #