data_7P2V
#
_model_server_result.job_id            JmAjgZlNXqWsNzDcq4zcSw 
_model_server_result.datetime_utc      '2024-12-01 01:01:36' 
_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          7p2v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":505}' 
#
_entry.id    7P2V 
#
_exptl.entry_id    7P2V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              468.011 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-[[(2S)-2-(4-chlorophenyl)-1'-methyl-spiro[2H-indole-3,4'-piperidine]-1-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide" 
_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            7P2V 
_cell.length_a            71.14 
_cell.length_b            71.14 
_cell.length_c            186.911 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7P2V 
_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    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                      5 
_struct_asym.id                             F 
_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 ASP 184 A ASP 184 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? 
metalc ? metalc2 A OD1 ASP 184 A ASP 184 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc3 A OD1 ASP 186 A ASP 186 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc4 A O ASP 186 A ASP 186 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? 
metalc ? metalc5 A ND1 HIS 188 A HIS 188 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc6 A O HIS 188 A HIS 188 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc7 A O PHE 197 A PHE 197 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? 
metalc ? metalc8 A O SER 200 A SER 200 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc9 A O VAL 203 A VAL 203 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc10 A OG SER 207 A SER 207 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.092 ? 
metalc ? metalc11 A O VAL 208 A VAL 208 1_555 C K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? 
metalc ? metalc12 A OG SER 243 A SER 243 1_555 D K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc13 A OD2 ASP 285 A ASP 285 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? 
metalc ? metalc14 B ZN ZN . A ZN 501 1_555 E O1 TLA . A TLA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc15 B ZN ZN . A ZN 501 1_555 E O2 TLA . A TLA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc16 D K K . A K 503 1_555 H O HOH . A HOH 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? 
#
_chem_comp.formula           'C25 H26 Cl N3 O2 S' 
_chem_comp.formula_weight    468.011 
_chem_comp.id                4XI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5-[[(2S)-2-(4-chlorophenyl)-1'-methyl-spiro[2H-indole-3,4'-piperidine]-1-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide" 
_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
O2 N2 4XI sing 1 n n 
N2 C13 4XI sing 2 n n 
O1 C13 4XI doub 3 n n 
C13 C11 4XI sing 4 n n 
CL1 C4 4XI sing 5 n n 
C11 C10 4XI doub 6 n y 
C11 S1 4XI sing 7 n y 
C10 C9 4XI sing 8 n y 
C3 C4 4XI doub 9 n y 
C3 C2 4XI sing 10 n y 
C4 C5 4XI sing 11 n y 
S1 C8 4XI sing 12 n y 
C9 C8 4XI doub 13 n y 
C2 C25 4XI doub 14 n y 
C8 C7 4XI sing 15 n n 
C5 C6 4XI doub 16 n y 
C25 C6 4XI sing 17 n y 
C25 C23 4XI sing 18 n n 
C7 N1 4XI sing 19 n n 
C14 C17 4XI sing 20 n n 
C14 C24 4XI sing 21 n n 
N1 C23 4XI sing 22 n n 
N1 C21 4XI sing 23 n n 
C23 C24 4XI sing 24 n n 
C20 C21 4XI doub 25 n y 
C20 C19 4XI sing 26 n y 
C17 N3 4XI sing 27 n n 
C21 C22 4XI sing 28 n y 
C19 C12 4XI doub 29 n y 
C24 C22 4XI sing 30 n n 
C24 C15 4XI sing 31 n n 
C22 C1 4XI doub 32 n y 
C12 C1 4XI sing 33 n y 
C18 N3 4XI sing 34 n n 
N3 C16 4XI sing 35 n n 
C16 C15 4XI sing 36 n n 
C1 H1 4XI sing 37 n n 
C2 H2 4XI sing 38 n n 
C3 H3 4XI sing 39 n n 
C5 H4 4XI sing 40 n n 
C6 H5 4XI sing 41 n n 
C7 H6 4XI sing 42 n n 
C7 H7 4XI sing 43 n n 
C10 H8 4XI sing 44 n n 
C12 H9 4XI sing 45 n n 
C14 H10 4XI sing 46 n n 
C14 H11 4XI sing 47 n n 
C15 H12 4XI sing 48 n n 
C15 H13 4XI sing 49 n n 
C16 H14 4XI sing 50 n n 
C16 H15 4XI sing 51 n n 
C17 H16 4XI sing 52 n n 
C17 H17 4XI sing 53 n n 
C19 H18 4XI sing 54 n n 
C23 H19 4XI sing 55 n n 
C18 H20 4XI sing 56 n n 
C18 H21 4XI sing 57 n n 
C18 H22 4XI sing 58 n n 
C20 H23 4XI sing 59 n n 
C9 H24 4XI sing 60 n n 
N2 H25 4XI sing 61 n n 
O2 H27 4XI sing 62 n n 
#
_atom_sites.entry_id                     7P2V 
_atom_sites.fract_transf_matrix[1][1]    0.014057 
_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]    0.014057 
_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]    0.00535 
_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 ZN A 1 501 501 ZN ZN . 
C 3 K A 1 502 601 K K . 
D 3 K A 1 503 602 K K . 
E 4 TLA A 1 504 701 TLA TLA . 
F 5 4XI A 1 505 702 4XI CTI . 
G 6 PEG A 1 506 703 PEG PEG . 
H 7 HOH A 1 601 157 HOH HOH . 
H 7 HOH A 2 602 156 HOH HOH . 
H 7 HOH A 3 603 60 HOH HOH . 
H 7 HOH A 4 604 68 HOH HOH . 
H 7 HOH A 5 605 49 HOH HOH . 
H 7 HOH A 6 606 44 HOH HOH . 
H 7 HOH A 7 607 33 HOH HOH . 
H 7 HOH A 8 608 90 HOH HOH . 
H 7 HOH A 9 609 146 HOH HOH . 
H 7 HOH A 10 610 87 HOH HOH . 
H 7 HOH A 11 611 54 HOH HOH . 
H 7 HOH A 12 612 153 HOH HOH . 
H 7 HOH A 13 613 19 HOH HOH . 
H 7 HOH A 14 614 17 HOH HOH . 
H 7 HOH A 15 615 85 HOH HOH . 
H 7 HOH A 16 616 38 HOH HOH . 
H 7 HOH A 17 617 5 HOH HOH . 
H 7 HOH A 18 618 37 HOH HOH . 
H 7 HOH A 19 619 110 HOH HOH . 
H 7 HOH A 20 620 18 HOH HOH . 
H 7 HOH A 21 621 132 HOH HOH . 
H 7 HOH A 22 622 155 HOH HOH . 
H 7 HOH A 23 623 20 HOH HOH . 
H 7 HOH A 24 624 10 HOH HOH . 
H 7 HOH A 25 625 97 HOH HOH . 
H 7 HOH A 26 626 13 HOH HOH . 
H 7 HOH A 27 627 48 HOH HOH . 
H 7 HOH A 28 628 82 HOH HOH . 
H 7 HOH A 29 629 45 HOH HOH . 
H 7 HOH A 30 630 35 HOH HOH . 
H 7 HOH A 31 631 6 HOH HOH . 
H 7 HOH A 32 632 99 HOH HOH . 
H 7 HOH A 33 633 28 HOH HOH . 
H 7 HOH A 34 634 7 HOH HOH . 
H 7 HOH A 35 635 46 HOH HOH . 
H 7 HOH A 36 636 4 HOH HOH . 
H 7 HOH A 37 637 1 HOH HOH . 
H 7 HOH A 38 638 61 HOH HOH . 
H 7 HOH A 39 639 39 HOH HOH . 
H 7 HOH A 40 640 59 HOH HOH . 
H 7 HOH A 41 641 67 HOH HOH . 
H 7 HOH A 42 642 9 HOH HOH . 
H 7 HOH A 43 643 78 HOH HOH . 
H 7 HOH A 44 644 24 HOH HOH . 
H 7 HOH A 45 645 23 HOH HOH . 
H 7 HOH A 46 646 22 HOH HOH . 
H 7 HOH A 47 647 66 HOH HOH . 
H 7 HOH A 48 648 149 HOH HOH . 
H 7 HOH A 49 649 14 HOH HOH . 
H 7 HOH A 50 650 74 HOH HOH . 
H 7 HOH A 51 651 11 HOH HOH . 
H 7 HOH A 52 652 84 HOH HOH . 
H 7 HOH A 53 653 2 HOH HOH . 
H 7 HOH A 54 654 41 HOH HOH . 
H 7 HOH A 55 655 25 HOH HOH . 
H 7 HOH A 56 656 15 HOH HOH . 
H 7 HOH A 57 657 140 HOH HOH . 
H 7 HOH A 58 658 62 HOH HOH . 
H 7 HOH A 59 659 26 HOH HOH . 
H 7 HOH A 60 660 47 HOH HOH . 
H 7 HOH A 61 661 81 HOH HOH . 
H 7 HOH A 62 662 133 HOH HOH . 
H 7 HOH A 63 663 27 HOH HOH . 
H 7 HOH A 64 664 3 HOH HOH . 
H 7 HOH A 65 665 148 HOH HOH . 
H 7 HOH A 66 666 79 HOH HOH . 
H 7 HOH A 67 667 58 HOH HOH . 
H 7 HOH A 68 668 40 HOH HOH . 
H 7 HOH A 69 669 29 HOH HOH . 
H 7 HOH A 70 670 43 HOH HOH . 
H 7 HOH A 71 671 116 HOH HOH . 
H 7 HOH A 72 672 55 HOH HOH . 
H 7 HOH A 73 673 53 HOH HOH . 
H 7 HOH A 74 674 86 HOH HOH . 
H 7 HOH A 75 675 126 HOH HOH . 
H 7 HOH A 76 676 105 HOH HOH . 
H 7 HOH A 77 677 108 HOH HOH . 
H 7 HOH A 78 678 57 HOH HOH . 
H 7 HOH A 79 679 111 HOH HOH . 
H 7 HOH A 80 680 8 HOH HOH . 
H 7 HOH A 81 681 71 HOH HOH . 
H 7 HOH A 82 682 12 HOH HOH . 
H 7 HOH A 83 683 154 HOH HOH . 
H 7 HOH A 84 684 21 HOH HOH . 
H 7 HOH A 85 685 106 HOH HOH . 
H 7 HOH A 86 686 70 HOH HOH . 
H 7 HOH A 87 687 72 HOH HOH . 
H 7 HOH A 88 688 42 HOH HOH . 
H 7 HOH A 89 689 98 HOH HOH . 
H 7 HOH A 90 690 88 HOH HOH . 
H 7 HOH A 91 691 73 HOH HOH . 
H 7 HOH A 92 692 137 HOH HOH . 
H 7 HOH A 93 693 138 HOH HOH . 
H 7 HOH A 94 694 117 HOH HOH . 
H 7 HOH A 95 695 152 HOH HOH . 
H 7 HOH A 96 696 141 HOH HOH . 
H 7 HOH A 97 697 50 HOH HOH . 
H 7 HOH A 98 698 124 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 4XI . . . F 5 -8.669 32.662 33.843 0.64 60.73 ? C1 4XI 505 A 1 
HETATM 2 C C2 4XI . . . F 5 -8.532 36.629 30.447 0.64 60.23 ? C2 4XI 505 A 1 
HETATM 3 C C3 4XI . . . F 5 -8.946 37.392 29.369 0.64 57.07 ? C3 4XI 505 A 1 
HETATM 4 C C4 4XI . . . F 5 -9.419 38.673 29.582 0.64 56.53 ? C4 4XI 505 A 1 
HETATM 5 C C5 4XI . . . F 5 -9.479 39.194 30.863 0.64 60.38 ? C5 4XI 505 A 1 
HETATM 6 C C6 4XI . . . F 5 -9.07 38.429 31.941 0.64 56.38 ? C6 4XI 505 A 1 
HETATM 7 C C7 4XI . . . F 5 -5.623 36.328 32.354 0.64 53.19 ? C7 4XI 505 A 1 
HETATM 8 C C8 4XI . . . F 5 -5.406 36.287 30.847 0.64 51.12 ? C8 4XI 505 A 1 
HETATM 9 C C10 4XI . . . F 5 -5.182 35.448 28.641 0.64 47.93 ? C10 4XI 505 A 1 
HETATM 10 C C11 4XI . . . F 5 -5.001 36.812 28.34 0.64 48.47 ? C11 4XI 505 A 1 
HETATM 11 C C12 4XI . . . F 5 -7.723 31.639 33.765 0.64 58.65 ? C12 4XI 505 A 1 
HETATM 12 C C13 4XI . . . F 5 -4.741 37.459 26.976 0.64 51.06 ? C13 4XI 505 A 1 
HETATM 13 C C14 4XI . . . F 5 -10.091 35.069 32.374 0.64 57.09 ? C14 4XI 505 A 1 
HETATM 14 C C15 4XI . . . F 5 -9.721 35.183 34.757 0.64 59.88 ? C15 4XI 505 A 1 
HETATM 15 C C16 4XI . . . F 5 -11.22 35.472 34.758 0.64 57.93 ? C16 4XI 505 A 1 
HETATM 16 C C17 4XI . . . F 5 -11.309 34.199 32.706 0.64 59.01 ? C17 4XI 505 A 1 
HETATM 17 C C19 4XI . . . F 5 -6.424 31.904 33.307 0.64 55.01 ? C19 4XI 505 A 1 
HETATM 18 C C21 4XI . . . F 5 -7.033 34.223 33.005 0.64 58.13 ? C21 4XI 505 A 1 
HETATM 19 C C22 4XI . . . F 5 -8.325 33.974 33.455 0.64 60.81 ? C22 4XI 505 A 1 
HETATM 20 C C23 4XI . . . F 5 -8.156 36.349 32.942 0.64 60.22 ? C23 4XI 505 A 1 
HETATM 21 C C25 4XI . . . F 5 -8.608 37.142 31.738 0.64 58.39 ? C25 4XI 505 A 1 
HETATM 22 C C18 4XI . . . F 5 -13.085 34.807 33.836 0.64 54.72 ? C18 4XI 505 A 1 
HETATM 23 C C20 4XI . . . F 5 -6.074 33.195 32.928 0.64 52.74 ? C20 4XI 505 A 1 
HETATM 24 C C24 4XI . . . F 5 -9.123 35.286 33.44 0.64 60.91 ? C24 4XI 505 A 1 
HETATM 25 C C9 4XI . . . F 5 -5.408 35.15 30.025 0.64 47.37 ? C9 4XI 505 A 1 
HETATM 26 N N1 4XI . . . F 5 -6.883 35.675 32.654 0.64 56.78 ? N1 4XI 505 A 1 
HETATM 27 N N2 4XI . . . F 5 -4.544 36.638 25.789 0.64 48.35 ? N2 4XI 505 A 1 
HETATM 28 N N3 4XI . . . F 5 -11.937 34.494 33.976 0.64 58.04 ? N3 4XI 505 A 1 
HETATM 29 O O1 4XI . . . F 5 -4.695 38.644 26.889 0.64 53.07 ? O1 4XI 505 A 1 
HETATM 30 O O2 4XI . . . F 5 -4.304 37.247 24.546 0.64 41.82 ? O2 4XI 505 A 1 
HETATM 31 S S1 4XI . . . F 5 -5.134 37.605 29.825 0.64 55.67 ? S1 4XI 505 A 1 
HETATM 32 CL CL1 4XI . . . F 5 -9.949 39.668 28.203 0.64 69.98 ? CL1 4XI 505 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#