data_1D4P # _model_server_result.job_id KI-d-elURpxBFpxJkDbKTg _model_server_result.datetime_utc '2024-10-24 04:32:33' _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 1d4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":400}' # _entry.id 1D4P # _exptl.entry_id 1D4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.452 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide _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 101.2 _cell.angle_gamma 90 _cell.entry_id 1D4P _cell.length_a 71.56 _cell.length_b 72.06 _cell.length_c 73.22 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 6 _struct_asym.id G _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 disulf ? disulf1 A SG CYS 9 A CYS 9 1_555 B SG CYS 119 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 B SG CYS 28 B CYS 64 1_555 B SG CYS 44 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 173 B CYS 209 1_555 B SG CYS 187 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 201 B CYS 237 1_555 B SG CYS 231 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 B ND2 ASN 53 B ASN 89 1_555 D C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 C C GLU 9 H GLU 308 1_555 C N TYS 10 H TYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 C C TYS 10 H TYS 309 1_555 C N LEU 11 H LEU 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 B O LYS 174 B LYS 210 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc2 B O THR 177 B THR 213 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 B O PHE 215 B PHE 251 4_446 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc4 B O ARG 233 B ARG 269 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc5 B O LYS 236 B LYS 272 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc6 E NA NA . B NA 398 1_555 I O HOH . B HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc7 E NA NA . B NA 398 1_555 I O HOH . B HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc8 E NA NA . B NA 398 1_555 I O HOH . B HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc9 F NA NA . B NA 399 1_555 I O HOH . B HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc10 F NA NA . B NA 399 1_555 I O HOH . B HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc11 F NA NA . B NA 399 1_555 I O HOH . B HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? # _chem_comp.formula 'C22 H24 N4 O' _chem_comp.formula_weight 360.452 _chem_comp.id BPP _chem_comp.mon_nstd_flag . _chem_comp.name 2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-amidinoindole-4-benzylpiperidin # _atom_sites.entry_id 1D4P _atom_sites.fract_transf_matrix[1][1] 0.013974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002767 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013877 _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] 0.013923 _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 D 4 NAG B 1 500 500 NAG NAG . E 5 NA B 1 398 398 NA NA . F 5 NA B 1 399 399 NA NA . G 6 BPP B 1 400 400 BPP BPP . H 7 HOH A 1 526 526 HOH HOH . H 7 HOH A 2 531 531 HOH HOH . H 7 HOH A 3 552 552 HOH HOH . H 7 HOH A 4 557 557 HOH HOH . H 7 HOH A 5 558 558 HOH HOH . H 7 HOH A 6 560 560 HOH HOH . H 7 HOH A 7 586 586 HOH HOH . H 7 HOH A 8 589 589 HOH HOH . H 7 HOH A 9 592 592 HOH HOH . H 7 HOH A 10 594 594 HOH HOH . H 7 HOH A 11 610 610 HOH HOH . H 7 HOH A 12 621 621 HOH HOH . H 7 HOH A 13 624 624 HOH HOH . H 7 HOH A 14 625 625 HOH HOH . I 7 HOH B 1 501 501 HOH HOH . I 7 HOH B 2 502 502 HOH HOH . I 7 HOH B 3 503 503 HOH HOH . I 7 HOH B 4 504 504 HOH HOH . I 7 HOH B 5 505 505 HOH HOH . I 7 HOH B 6 506 506 HOH HOH . I 7 HOH B 7 507 507 HOH HOH . I 7 HOH B 8 508 508 HOH HOH . I 7 HOH B 9 509 509 HOH HOH . I 7 HOH B 10 510 510 HOH HOH . I 7 HOH B 11 511 511 HOH HOH . I 7 HOH B 12 512 512 HOH HOH . I 7 HOH B 13 513 513 HOH HOH . I 7 HOH B 14 514 514 HOH HOH . I 7 HOH B 15 515 515 HOH HOH . I 7 HOH B 16 516 516 HOH HOH . I 7 HOH B 17 517 517 HOH HOH . I 7 HOH B 18 518 518 HOH HOH . I 7 HOH B 19 519 519 HOH HOH . I 7 HOH B 20 520 520 HOH HOH . I 7 HOH B 21 521 521 HOH HOH . I 7 HOH B 22 522 522 HOH HOH . I 7 HOH B 23 523 523 HOH HOH . I 7 HOH B 24 524 524 HOH HOH . I 7 HOH B 25 525 525 HOH HOH . I 7 HOH B 26 527 527 HOH HOH . I 7 HOH B 27 528 528 HOH HOH . I 7 HOH B 28 529 529 HOH HOH . I 7 HOH B 29 530 530 HOH HOH . I 7 HOH B 30 532 532 HOH HOH . I 7 HOH B 31 533 533 HOH HOH . I 7 HOH B 32 534 534 HOH HOH . I 7 HOH B 33 535 535 HOH HOH . I 7 HOH B 34 536 536 HOH HOH . I 7 HOH B 35 537 537 HOH HOH . I 7 HOH B 36 538 538 HOH HOH . I 7 HOH B 37 539 539 HOH HOH . I 7 HOH B 38 540 540 HOH HOH . I 7 HOH B 39 541 541 HOH HOH . I 7 HOH B 40 542 542 HOH HOH . I 7 HOH B 41 543 543 HOH HOH . I 7 HOH B 42 544 544 HOH HOH . I 7 HOH B 43 545 545 HOH HOH . I 7 HOH B 44 546 546 HOH HOH . I 7 HOH B 45 547 547 HOH HOH . I 7 HOH B 46 548 548 HOH HOH . I 7 HOH B 47 549 549 HOH HOH . I 7 HOH B 48 550 550 HOH HOH . I 7 HOH B 49 551 551 HOH HOH . I 7 HOH B 50 553 553 HOH HOH . I 7 HOH B 51 554 554 HOH HOH . I 7 HOH B 52 555 555 HOH HOH . I 7 HOH B 53 556 556 HOH HOH . I 7 HOH B 54 559 559 HOH HOH . I 7 HOH B 55 561 561 HOH HOH . I 7 HOH B 56 562 562 HOH HOH . I 7 HOH B 57 563 563 HOH HOH . I 7 HOH B 58 564 564 HOH HOH . I 7 HOH B 59 565 565 HOH HOH . I 7 HOH B 60 566 566 HOH HOH . I 7 HOH B 61 567 567 HOH HOH . I 7 HOH B 62 568 568 HOH HOH . I 7 HOH B 63 569 569 HOH HOH . I 7 HOH B 64 570 570 HOH HOH . I 7 HOH B 65 571 571 HOH HOH . I 7 HOH B 66 572 572 HOH HOH . I 7 HOH B 67 573 573 HOH HOH . I 7 HOH B 68 575 575 HOH HOH . I 7 HOH B 69 576 576 HOH HOH . I 7 HOH B 70 577 577 HOH HOH . I 7 HOH B 71 578 578 HOH HOH . I 7 HOH B 72 579 579 HOH HOH . I 7 HOH B 73 581 581 HOH HOH . I 7 HOH B 74 582 582 HOH HOH . I 7 HOH B 75 583 583 HOH HOH . I 7 HOH B 76 584 584 HOH HOH . I 7 HOH B 77 588 588 HOH HOH . I 7 HOH B 78 590 590 HOH HOH . I 7 HOH B 79 591 591 HOH HOH . I 7 HOH B 80 593 593 HOH HOH . I 7 HOH B 81 595 595 HOH HOH . I 7 HOH B 82 596 596 HOH HOH . I 7 HOH B 83 599 599 HOH HOH . I 7 HOH B 84 600 600 HOH HOH . I 7 HOH B 85 601 601 HOH HOH . I 7 HOH B 86 603 603 HOH HOH . I 7 HOH B 87 604 604 HOH HOH . I 7 HOH B 88 605 605 HOH HOH . I 7 HOH B 89 609 609 HOH HOH . I 7 HOH B 90 612 612 HOH HOH . I 7 HOH B 91 613 613 HOH HOH . I 7 HOH B 92 614 614 HOH HOH . I 7 HOH B 93 615 615 HOH HOH . I 7 HOH B 94 616 616 HOH HOH . I 7 HOH B 95 617 617 HOH HOH . I 7 HOH B 96 618 618 HOH HOH . I 7 HOH B 97 619 619 HOH HOH . I 7 HOH B 98 620 620 HOH HOH . I 7 HOH B 99 622 622 HOH HOH . I 7 HOH B 100 623 623 HOH HOH . I 7 HOH B 101 626 626 HOH HOH . I 7 HOH B 102 627 627 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 C1 BPP . . . G 6 -23.977 -31.842 23.185 1 18.1 ? C1 BPP 400 B 1 HETATM 2 C C2 BPP . . . G 6 -23.262 -33.049 22.846 1 17.18 ? C2 BPP 400 B 1 HETATM 3 C C3 BPP . . . G 6 -22.241 -32.969 21.857 1 16.38 ? C3 BPP 400 B 1 HETATM 4 C C4 BPP . . . G 6 -21.939 -31.736 21.219 1 18.56 ? C4 BPP 400 B 1 HETATM 5 C C5 BPP . . . G 6 -22.654 -30.55 21.562 1 17.75 ? C5 BPP 400 B 1 HETATM 6 C C6 BPP . . . G 6 -23.672 -30.618 22.539 1 17.4 ? C6 BPP 400 B 1 HETATM 7 C C10 BPP . . . G 6 -21.361 -33.891 21.303 1 18.94 ? C10 BPP 400 B 1 HETATM 8 C C11 BPP . . . G 6 -20.55 -33.242 20.366 1 19.91 ? C11 BPP 400 B 1 HETATM 9 N N12 BPP . . . G 6 -20.95 -31.931 20.363 1 16.67 ? N12 BPP 400 B 1 HETATM 10 C C13 BPP . . . G 6 -24.987 -31.838 24.186 1 18.13 ? C13 BPP 400 B 1 HETATM 11 N N14 BPP . . . G 6 -25.122 -30.703 24.844 1 20.67 ? N14 BPP 400 B 1 HETATM 12 N N15 BPP . . . G 6 -25.73 -32.884 24.466 1 19.67 ? N15 BPP 400 B 1 HETATM 13 C C17 BPP . . . G 6 -19.479 -33.753 19.558 1 20.75 ? C17 BPP 400 B 1 HETATM 14 O O18 BPP . . . G 6 -19.665 -34.337 18.48 1 23.09 ? O18 BPP 400 B 1 HETATM 15 N N19 BPP . . . G 6 -18.094 -33.561 20.061 1 20.39 ? N19 BPP 400 B 1 HETATM 16 C C20 BPP . . . G 6 -16.853 -34.06 19.319 1 23.08 ? C20 BPP 400 B 1 HETATM 17 C C21 BPP . . . G 6 -16.392 -35.256 20.202 1 20.18 ? C21 BPP 400 B 1 HETATM 18 C C22 BPP . . . G 6 -16.129 -34.771 21.628 1 19.62 ? C22 BPP 400 B 1 HETATM 19 C C23 BPP . . . G 6 -17.395 -34.016 22.227 1 20.73 ? C23 BPP 400 B 1 HETATM 20 C C24 BPP . . . G 6 -17.791 -32.896 21.325 1 20.92 ? C24 BPP 400 B 1 HETATM 21 C C33 BPP . . . G 6 -15.72 -35.925 22.6 1 19.68 ? C33 BPP 400 B 1 HETATM 22 C C35 BPP . . . G 6 -15.246 -35.36 23.973 1 20.23 ? C35 BPP 400 B 1 HETATM 23 C C38 BPP . . . G 6 -16.13 -35.317 25.124 1 20.45 ? C38 BPP 400 B 1 HETATM 24 C C39 BPP . . . G 6 -15.699 -34.801 26.36 1 24.14 ? C39 BPP 400 B 1 HETATM 25 C C40 BPP . . . G 6 -14.374 -34.32 26.464 1 23.56 ? C40 BPP 400 B 1 HETATM 26 C C41 BPP . . . G 6 -13.487 -34.351 25.355 1 21.64 ? C41 BPP 400 B 1 HETATM 27 C C42 BPP . . . G 6 -13.914 -34.864 24.126 1 20.71 ? C42 BPP 400 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #