data_6G40
#
_model_server_result.job_id            s3VpmWlVMyH037RrUHoFoQ 
_model_server_result.datetime_utc      '2025-06-21 19:39:06' 
_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          6g40 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    6G40 
#
_exptl.entry_id    6G40 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              410.466 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N}-(3-methoxy-4-methyl-phenyl)-4-(4-methoxy-2-oxidanylidene-3~{H}-benzimidazol-1-yl)piperidine-1-carboxamide 
_entity.pdbx_number_of_molecules    3 
_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            6G40 
_cell.length_a            80.86 
_cell.length_b            81.335 
_cell.length_c            168.593 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6G40 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,M 1 1 
B,H,I,J,N 2 1 
C,K,L,O 3 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
? 2 D N N 
? 2 H N N 
? 2 K N 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 NE2 HIS 269 A HIS 276 1_555 F NI NI . A NI 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc2 A NE2 HIS 275 A HIS 282 1_555 F NI NI . A NI 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc3 F NI NI . A NI 403 1_555 B NE2 HIS 269 B HIS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? 
metalc ? metalc4 F NI NI . A NI 403 1_555 B NE2 HIS 275 B HIS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc5 F NI NI . A NI 403 1_555 C NE2 HIS 269 C HIS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc6 F NI NI . A NI 403 1_555 C NE2 HIS 275 C HIS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
#
_chem_comp.formula           'C22 H26 N4 O4' 
_chem_comp.formula_weight    410.466 
_chem_comp.id                ELK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N}-(3-methoxy-4-methyl-phenyl)-4-(4-methoxy-2-oxidanylidene-3~{H}-benzimidazol-1-yl)piperidine-1-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
C01 O02 ELK sing 89 n n 
O02 C03 ELK sing 90 n n 
C03 C04 ELK doub 91 n y 
C03 C08 ELK sing 92 n y 
N09 C08 ELK sing 93 n n 
N09 C10 ELK sing 94 n n 
C04 C05 ELK sing 95 n y 
C08 C07 ELK doub 96 n y 
O11 C10 ELK doub 97 n n 
C10 N12 ELK sing 98 n n 
C05 C06 ELK doub 99 n y 
C07 N12 ELK sing 100 n n 
C07 C06 ELK sing 101 n y 
N12 C13 ELK sing 102 n n 
C14 C13 ELK sing 103 n n 
C14 C15 ELK sing 104 n n 
C13 C18 ELK sing 105 n n 
C15 N16 ELK sing 106 n n 
C18 C17 ELK sing 107 n n 
N16 C17 ELK sing 108 n n 
N16 C19 ELK sing 109 n n 
O20 C19 ELK doub 110 n n 
C19 N21 ELK sing 111 n n 
N21 C22 ELK sing 112 n n 
C22 C30 ELK doub 113 n y 
C22 C23 ELK sing 114 n y 
C30 C29 ELK sing 115 n y 
C23 C24 ELK doub 116 n y 
C26 O25 ELK sing 117 n n 
C29 C27 ELK doub 118 n y 
C24 C27 ELK sing 119 n y 
C24 O25 ELK sing 120 n n 
C27 C28 ELK sing 121 n n 
C13 H1 ELK sing 122 n n 
C15 H2 ELK sing 123 n n 
C15 H3 ELK sing 124 n n 
C17 H4 ELK sing 125 n n 
C17 H5 ELK sing 126 n n 
C26 H6 ELK sing 127 n n 
C26 H7 ELK sing 128 n n 
C26 H8 ELK sing 129 n n 
C28 H9 ELK sing 130 n n 
C28 H10 ELK sing 131 n n 
C28 H11 ELK sing 132 n n 
C01 H12 ELK sing 133 n n 
C01 H13 ELK sing 134 n n 
C01 H14 ELK sing 135 n n 
C04 H15 ELK sing 136 n n 
C05 H16 ELK sing 137 n n 
C06 H17 ELK sing 138 n n 
N09 H18 ELK sing 139 n n 
C14 H19 ELK sing 140 n n 
C14 H20 ELK sing 141 n n 
C18 H21 ELK sing 142 n n 
C18 H22 ELK sing 143 n n 
N21 H23 ELK sing 144 n n 
C23 H24 ELK sing 145 n n 
C29 H25 ELK sing 146 n n 
C30 H26 ELK sing 147 n n 
#
_atom_sites.entry_id                     6G40 
_atom_sites.fract_transf_matrix[1][1]    0.012367 
_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]    0.012295 
_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]    0.005931 
_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 2 ELK A 1 401 1 ELK LIG . 
E 3 PEG A 1 402 1 PEG PEG . 
F 4 NI A 1 403 1 NI NI . 
G 5 ACT A 1 404 4 ACT ACT . 
H 2 ELK B 1 401 2 ELK LIG . 
I 5 ACT B 1 402 1 ACT ACT . 
J 5 ACT B 1 403 3 ACT ACT . 
K 2 ELK C 1 401 3 ELK LIG . 
L 5 ACT C 1 402 2 ACT ACT . 
M 6 HOH A 1 501 98 HOH HOH . 
M 6 HOH A 2 502 105 HOH HOH . 
M 6 HOH A 3 503 109 HOH HOH . 
M 6 HOH A 4 504 107 HOH HOH . 
M 6 HOH A 5 505 137 HOH HOH . 
M 6 HOH A 6 506 52 HOH HOH . 
M 6 HOH A 7 507 57 HOH HOH . 
M 6 HOH A 8 508 92 HOH HOH . 
M 6 HOH A 9 509 38 HOH HOH . 
M 6 HOH A 10 510 71 HOH HOH . 
M 6 HOH A 11 511 93 HOH HOH . 
M 6 HOH A 12 512 85 HOH HOH . 
M 6 HOH A 13 513 78 HOH HOH . 
M 6 HOH A 14 514 72 HOH HOH . 
M 6 HOH A 15 515 110 HOH HOH . 
M 6 HOH A 16 516 88 HOH HOH . 
M 6 HOH A 17 517 134 HOH HOH . 
M 6 HOH A 18 518 81 HOH HOH . 
M 6 HOH A 19 519 108 HOH HOH . 
M 6 HOH A 20 520 18 HOH HOH . 
M 6 HOH A 21 521 77 HOH HOH . 
M 6 HOH A 22 522 74 HOH HOH . 
M 6 HOH A 23 523 49 HOH HOH . 
M 6 HOH A 24 524 86 HOH HOH . 
M 6 HOH A 25 525 39 HOH HOH . 
M 6 HOH A 26 526 37 HOH HOH . 
M 6 HOH A 27 527 111 HOH HOH . 
M 6 HOH A 28 528 70 HOH HOH . 
M 6 HOH A 29 529 51 HOH HOH . 
M 6 HOH A 30 530 21 HOH HOH . 
M 6 HOH A 31 531 48 HOH HOH . 
M 6 HOH A 32 532 50 HOH HOH . 
M 6 HOH A 33 533 34 HOH HOH . 
M 6 HOH A 34 534 126 HOH HOH . 
M 6 HOH A 35 535 139 HOH HOH . 
M 6 HOH A 36 536 97 HOH HOH . 
M 6 HOH A 37 537 20 HOH HOH . 
M 6 HOH A 38 538 13 HOH HOH . 
M 6 HOH A 39 539 17 HOH HOH . 
M 6 HOH A 40 540 1 HOH HOH . 
M 6 HOH A 41 541 90 HOH HOH . 
M 6 HOH A 42 542 22 HOH HOH . 
M 6 HOH A 43 543 75 HOH HOH . 
M 6 HOH A 44 544 82 HOH HOH . 
M 6 HOH A 45 545 73 HOH HOH . 
M 6 HOH A 46 546 136 HOH HOH . 
M 6 HOH A 47 547 91 HOH HOH . 
M 6 HOH A 48 548 106 HOH HOH . 
M 6 HOH A 49 549 19 HOH HOH . 
N 6 HOH B 1 501 114 HOH HOH . 
N 6 HOH B 2 502 14 HOH HOH . 
N 6 HOH B 3 503 9 HOH HOH . 
N 6 HOH B 4 504 4 HOH HOH . 
N 6 HOH B 5 505 62 HOH HOH . 
N 6 HOH B 6 506 8 HOH HOH . 
N 6 HOH B 7 507 44 HOH HOH . 
N 6 HOH B 8 508 6 HOH HOH . 
N 6 HOH B 9 509 54 HOH HOH . 
N 6 HOH B 10 510 117 HOH HOH . 
N 6 HOH B 11 511 45 HOH HOH . 
N 6 HOH B 12 512 41 HOH HOH . 
N 6 HOH B 13 513 102 HOH HOH . 
N 6 HOH B 14 514 69 HOH HOH . 
N 6 HOH B 15 515 58 HOH HOH . 
N 6 HOH B 16 516 133 HOH HOH . 
N 6 HOH B 17 517 89 HOH HOH . 
N 6 HOH B 18 518 24 HOH HOH . 
N 6 HOH B 19 519 56 HOH HOH . 
N 6 HOH B 20 520 120 HOH HOH . 
N 6 HOH B 21 521 31 HOH HOH . 
N 6 HOH B 22 522 47 HOH HOH . 
N 6 HOH B 23 523 10 HOH HOH . 
N 6 HOH B 24 524 135 HOH HOH . 
N 6 HOH B 25 525 129 HOH HOH . 
N 6 HOH B 26 526 127 HOH HOH . 
N 6 HOH B 27 527 121 HOH HOH . 
N 6 HOH B 28 528 32 HOH HOH . 
N 6 HOH B 29 529 23 HOH HOH . 
N 6 HOH B 30 530 132 HOH HOH . 
N 6 HOH B 31 531 7 HOH HOH . 
O 6 HOH C 1 501 66 HOH HOH . 
O 6 HOH C 2 502 131 HOH HOH . 
O 6 HOH C 3 503 63 HOH HOH . 
O 6 HOH C 4 504 124 HOH HOH . 
O 6 HOH C 5 505 55 HOH HOH . 
O 6 HOH C 6 506 5 HOH HOH . 
O 6 HOH C 7 507 64 HOH HOH . 
O 6 HOH C 8 508 26 HOH HOH . 
O 6 HOH C 9 509 76 HOH HOH . 
O 6 HOH C 10 510 99 HOH HOH . 
O 6 HOH C 11 511 3 HOH HOH . 
O 6 HOH C 12 512 43 HOH HOH . 
O 6 HOH C 13 513 87 HOH HOH . 
O 6 HOH C 14 514 95 HOH HOH . 
O 6 HOH C 15 515 68 HOH HOH . 
O 6 HOH C 16 516 141 HOH HOH . 
O 6 HOH C 17 517 138 HOH HOH . 
O 6 HOH C 18 518 130 HOH HOH . 
O 6 HOH C 19 519 140 HOH HOH . 
O 6 HOH C 20 520 123 HOH HOH . 
O 6 HOH C 21 521 67 HOH HOH . 
O 6 HOH C 22 522 128 HOH HOH . 
O 6 HOH C 23 523 101 HOH HOH . 
O 6 HOH C 24 524 142 HOH HOH . 
O 6 HOH C 25 525 125 HOH HOH . 
O 6 HOH C 26 526 33 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 C10 ELK . . . D 2 6.041 14.285 24.55 1 63.39 ? C10 ELK 401 A 1 
HETATM 2 N N12 ELK . . . D 2 5.865 13.371 25.622 1 61.96 ? N12 ELK 401 A 1 
HETATM 3 C C13 ELK . . . D 2 5.365 13.558 26.987 1 58.73 ? C13 ELK 401 A 1 
HETATM 4 C C15 ELK . . . D 2 3.037 13.72 27.996 1 56.31 ? C15 ELK 401 A 1 
HETATM 5 C C17 ELK . . . D 2 4.935 14.361 29.324 1 57.56 ? C17 ELK 401 A 1 
HETATM 6 C C22 ELK . . . D 2 5.22 10.34 31.159 1 56.04 ? C22 ELK 401 A 1 
HETATM 7 C C24 ELK . . . D 2 6.974 8.783 31.894 1 57.38 ? C24 ELK 401 A 1 
HETATM 8 C C26 ELK . . . D 2 9.348 9.272 31.643 1 59.6 ? C26 ELK 401 A 1 
HETATM 9 C C28 ELK . . . D 2 6.396 6.402 32.7 1 60.49 ? C28 ELK 401 A 1 
HETATM 10 C C01 ELK . . . D 2 8.91 10.64 21.45 1 67.65 ? C01 ELK 401 A 1 
HETATM 11 O O02 ELK . . . D 2 7.675 11.206 21.79 1 66.73 ? O02 ELK 401 A 1 
HETATM 12 C C03 ELK . . . D 2 7.253 11.073 23.137 1 64.29 ? C03 ELK 401 A 1 
HETATM 13 C C04 ELK . . . D 2 7.31 9.822 23.785 1 63.64 ? C04 ELK 401 A 1 
HETATM 14 C C05 ELK . . . D 2 6.883 9.696 25.108 1 62.45 ? C05 ELK 401 A 1 
HETATM 15 C C06 ELK . . . D 2 6.389 10.812 25.798 1 60.78 ? C06 ELK 401 A 1 
HETATM 16 C C07 ELK . . . D 2 6.323 12.078 25.156 1 62.58 ? C07 ELK 401 A 1 
HETATM 17 C C08 ELK . . . D 2 6.751 12.203 23.838 1 63.5 ? C08 ELK 401 A 1 
HETATM 18 N N09 ELK . . . D 2 6.582 13.575 23.448 1 62.65 ? N09 ELK 401 A 1 
HETATM 19 O O11 ELK . . . D 2 5.781 15.452 24.539 1 66.97 ? O11 ELK 401 A 1 
HETATM 20 C C14 ELK . . . D 2 3.891 13.778 26.684 1 56.4 ? C14 ELK 401 A 1 
HETATM 21 N N16 ELK . . . D 2 3.964 13.306 29.047 1 55.38 ? N16 ELK 401 A 1 
HETATM 22 C C18 ELK . . . D 2 5.846 14.474 28.087 1 58.61 ? C18 ELK 401 A 1 
HETATM 23 C C19 ELK . . . D 2 4.027 11.973 29.596 1 55.87 ? C19 ELK 401 A 1 
HETATM 24 O O20 ELK . . . D 2 3.214 11.146 29.249 1 56.29 ? O20 ELK 401 A 1 
HETATM 25 N N21 ELK . . . D 2 5.047 11.64 30.604 1 56.7 ? N21 ELK 401 A 1 
HETATM 26 C C23 ELK . . . D 2 6.581 10.036 31.393 1 56.78 ? C23 ELK 401 A 1 
HETATM 27 O O25 ELK . . . D 2 8.311 8.469 32.168 1 57.96 ? O25 ELK 401 A 1 
HETATM 28 C C27 ELK . . . D 2 5.98 7.809 32.143 1 59.28 ? C27 ELK 401 A 1 
HETATM 29 C C29 ELK . . . D 2 4.628 8.096 31.883 1 59.43 ? C29 ELK 401 A 1 
HETATM 30 C C30 ELK . . . D 2 4.233 9.364 31.375 1 56.87 ? C30 ELK 401 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           30 
#