data_7LMY
#
_model_server_result.job_id            e2CEJN6owsdHCcu5MJTAAw 
_model_server_result.datetime_utc      '2024-11-22 02:41:15' 
_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          7lmy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":903}' 
#
_entry.id    7LMY 
#
_exptl.entry_id    7LMY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              520.666 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine 
_entity.pdbx_number_of_molecules    6 
_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            7LMY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LMY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA 
_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    ? 
_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
? 3 I N N 
? 3 N N N 
? 3 S N N 
? 3 X N N 
? 3 CA N N 
? 3 HA 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 OG1 THR 252 A THR 252 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc2 G O3G ATP . A ATP 901 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc3 G O2B ATP . A ATP 901 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc4 H O2G ATP . A ATP 902 1_555 K MG MG . A MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc5 H O1A ATP . A ATP 902 1_555 K MG MG . A MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc6 B OG1 THR 252 B THR 252 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc7 L O3G ATP . B ATP 901 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc8 L O2B ATP . B ATP 901 1_555 O MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc9 M O2G ATP . B ATP 902 1_555 P MG MG . B MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc10 M O1A ATP . B ATP 902 1_555 P MG MG . B MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc11 C OG1 THR 252 C THR 252 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc12 Q O3G ATP . C ATP 901 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc13 Q O2B ATP . C ATP 901 1_555 T MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc14 R O2G ATP . C ATP 902 1_555 U MG MG . C MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc15 R O1A ATP . C ATP 902 1_555 U MG MG . C MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc16 D OG1 THR 252 D THR 252 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc17 V O3G ATP . D ATP 901 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? 
metalc ? metalc18 V O2B ATP . D ATP 901 1_555 Y MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc19 W O2G ATP . D ATP 902 1_555 Z MG MG . D MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc20 W O1A ATP . D ATP 902 1_555 Z MG MG . D MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc21 E OG1 THR 252 E THR 252 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
metalc ? metalc22 AA O3G ATP . E ATP 901 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc23 AA O2B ATP . E ATP 901 1_555 DA MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? 
metalc ? metalc24 BA O2G ATP . E ATP 902 1_555 EA MG MG . E MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc25 BA O1A ATP . E ATP 902 1_555 EA MG MG . E MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc26 F OG1 THR 252 F THR 252 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc27 FA O3G ATP . F ATP 901 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc28 FA O2B ATP . F ATP 901 1_555 IA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? 
metalc ? metalc29 GA O2G ATP . F ATP 902 1_555 JA MG MG . F MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc30 GA O1A ATP . F ATP 902 1_555 JA MG MG . F MG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
#
_chem_comp.formula           'C27 H28 N4 O3 S2' 
_chem_comp.formula_weight    520.666 
_chem_comp.id                Y6Y 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine 
_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
C24 N3 Y6Y doub 423 n y 
C24 C25 Y6Y sing 424 n y 
N3 C23 Y6Y sing 425 n y 
O S Y6Y doub 426 n n 
O1 S Y6Y doub 427 n n 
C9 C8 Y6Y doub 428 n y 
C9 C10 Y6Y sing 429 n y 
C25 C26 Y6Y doub 430 n y 
C8 C7 Y6Y sing 431 n y 
S C10 Y6Y sing 432 n n 
S C13 Y6Y sing 433 n n 
C23 C22 Y6Y doub 434 n y 
C10 C11 Y6Y doub 435 n y 
C26 C22 Y6Y sing 436 n y 
C7 C6 Y6Y sing 437 n n 
C7 C12 Y6Y doub 438 n y 
C22 N2 Y6Y sing 439 n n 
C11 C12 Y6Y sing 440 n y 
C6 C5 Y6Y doub 441 n y 
C6 C1 Y6Y sing 442 n y 
C C1 Y6Y sing 443 n n 
C5 C4 Y6Y sing 444 n y 
C1 C2 Y6Y doub 445 n y 
C4 C3 Y6Y doub 446 n y 
C2 C3 Y6Y sing 447 n y 
C20 C19 Y6Y sing 448 n n 
C20 C21 Y6Y sing 449 n n 
C3 O2 Y6Y sing 450 n n 
S1 C16 Y6Y sing 451 n n 
S1 C17 Y6Y sing 452 n n 
N2 C16 Y6Y sing 453 n y 
N2 C15 Y6Y sing 454 n y 
C19 C18 Y6Y sing 455 n n 
O2 C14 Y6Y sing 456 n n 
C14 C15 Y6Y sing 457 n n 
C21 C17 Y6Y sing 458 n n 
C16 N1 Y6Y doub 459 n y 
C15 N Y6Y doub 460 n y 
C18 C17 Y6Y sing 461 n n 
N1 N Y6Y sing 462 n y 
C8 H1 Y6Y sing 463 n n 
C5 H2 Y6Y sing 464 n n 
C2 H3 Y6Y sing 465 n n 
C9 H4 Y6Y sing 466 n n 
C11 H5 Y6Y sing 467 n n 
C H6 Y6Y sing 468 n n 
C H7 Y6Y sing 469 n n 
C H8 Y6Y sing 470 n n 
C12 H9 Y6Y sing 471 n n 
C13 H10 Y6Y sing 472 n n 
C13 H11 Y6Y sing 473 n n 
C13 H12 Y6Y sing 474 n n 
C14 H13 Y6Y sing 475 n n 
C14 H14 Y6Y sing 476 n n 
C17 H15 Y6Y sing 477 n n 
C18 H16 Y6Y sing 478 n n 
C18 H17 Y6Y sing 479 n n 
C19 H18 Y6Y sing 480 n n 
C19 H19 Y6Y sing 481 n n 
C20 H20 Y6Y sing 482 n n 
C20 H21 Y6Y sing 483 n n 
C21 H22 Y6Y sing 484 n n 
C21 H23 Y6Y sing 485 n n 
C23 H24 Y6Y sing 486 n n 
C24 H25 Y6Y sing 487 n n 
C25 H26 Y6Y sing 488 n n 
C26 H27 Y6Y sing 489 n n 
C4 H28 Y6Y sing 490 n n 
#
_atom_sites.entry_id                     7LMY 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
G 2 ATP A 1 901 801 ATP ATP . 
H 2 ATP A 1 902 901 ATP ATP . 
I 3 Y6Y A 1 903 1001 Y6Y NM3 . 
J 4 MG A 1 904 1 MG MG . 
K 4 MG A 1 905 7 MG MG . 
L 2 ATP B 1 901 801 ATP ATP . 
M 2 ATP B 1 902 901 ATP ATP . 
N 3 Y6Y B 1 903 1001 Y6Y NM3 . 
O 4 MG B 1 904 8 MG MG . 
P 4 MG B 1 905 9 MG MG . 
Q 2 ATP C 1 901 801 ATP ATP . 
R 2 ATP C 1 902 901 ATP ATP . 
S 3 Y6Y C 1 903 1001 Y6Y NM3 . 
T 4 MG C 1 904 10 MG MG . 
U 4 MG C 1 905 11 MG MG . 
V 2 ATP D 1 901 801 ATP ATP . 
W 2 ATP D 1 902 901 ATP ATP . 
X 3 Y6Y D 1 903 1001 Y6Y NM3 . 
Y 4 MG D 1 904 12 MG MG . 
Z 4 MG D 1 905 13 MG MG . 
AA 2 ATP E 1 901 801 ATP ATP . 
BA 2 ATP E 1 902 901 ATP ATP . 
CA 3 Y6Y E 1 903 1001 Y6Y NM3 . 
DA 4 MG E 1 904 14 MG MG . 
EA 4 MG E 1 905 15 MG MG . 
FA 2 ATP F 1 901 801 ATP ATP . 
GA 2 ATP F 1 902 901 ATP ATP . 
HA 3 Y6Y F 1 903 1001 Y6Y NM3 . 
IA 4 MG F 1 904 16 MG MG . 
JA 4 MG F 1 905 17 MG MG . 
#
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 N N1 Y6Y . . . S 3 199.025 137.142 151.924 1 14.83 ? N1 Y6Y 903 C 1 
HETATM 2 C C8 Y6Y . . . S 3 208.005 141.698 147.566 1 14.83 ? C8 Y6Y 903 C 1 
HETATM 3 C C5 Y6Y . . . S 3 204.943 142.058 149.373 1 14.83 ? C5 Y6Y 903 C 1 
HETATM 4 C C6 Y6Y . . . S 3 206.095 141.31 149.168 1 14.83 ? C6 Y6Y 903 C 1 
HETATM 5 C C2 Y6Y . . . S 3 204.829 139.273 149.805 1 14.83 ? C2 Y6Y 903 C 1 
HETATM 6 C C9 Y6Y . . . S 3 209.152 142.389 147.195 1 14.83 ? C9 Y6Y 903 C 1 
HETATM 7 C C10 Y6Y . . . S 3 209.628 143.42 147.994 1 14.83 ? C10 Y6Y 903 C 1 
HETATM 8 C C11 Y6Y . . . S 3 208.955 143.759 149.161 1 14.83 ? C11 Y6Y 903 C 1 
HETATM 9 C C3 Y6Y . . . S 3 203.703 140.067 149.988 1 14.83 ? C3 Y6Y 903 C 1 
HETATM 10 N N Y6Y . . . S 3 200.434 137.256 151.985 1 14.83 ? N Y6Y 903 C 1 
HETATM 11 C C Y6Y . . . S 3 207.231 138.95 149.217 1 14.83 ? C Y6Y 903 C 1 
HETATM 12 O O Y6Y . . . S 3 211.715 143.428 146.659 1 14.83 ? O Y6Y 903 C 1 
HETATM 13 C C1 Y6Y . . . S 3 206.033 139.84 149.403 1 14.83 ? C1 Y6Y 903 C 1 
HETATM 14 C C12 Y6Y . . . S 3 207.81 143.065 149.53 1 14.83 ? C12 Y6Y 903 C 1 
HETATM 15 C C13 Y6Y . . . S 3 211.839 144.572 148.92 1 14.83 ? C13 Y6Y 903 C 1 
HETATM 16 C C14 Y6Y . . . S 3 202.345 138.096 150.489 1 14.83 ? C14 Y6Y 903 C 1 
HETATM 17 C C15 Y6Y . . . S 3 200.901 137.805 150.828 1 14.83 ? C15 Y6Y 903 C 1 
HETATM 18 C C16 Y6Y . . . S 3 198.724 137.63 150.712 1 14.83 ? C16 Y6Y 903 C 1 
HETATM 19 C C17 Y6Y . . . S 3 195.992 136.91 151.173 1 14.83 ? C17 Y6Y 903 C 1 
HETATM 20 C C18 Y6Y . . . S 3 196.279 135.415 151.151 1 14.83 ? C18 Y6Y 903 C 1 
HETATM 21 C C19 Y6Y . . . S 3 195.26 134.768 150.223 1 14.83 ? C19 Y6Y 903 C 1 
HETATM 22 C C20 Y6Y . . . S 3 194.225 135.827 149.869 1 14.83 ? C20 Y6Y 903 C 1 
HETATM 23 C C21 Y6Y . . . S 3 194.563 137.071 150.678 1 14.83 ? C21 Y6Y 903 C 1 
HETATM 24 C C22 Y6Y . . . S 3 199.828 138.545 148.847 1 14.83 ? C22 Y6Y 903 C 1 
HETATM 25 C C23 Y6Y . . . S 3 199.567 137.781 147.711 1 14.83 ? C23 Y6Y 903 C 1 
HETATM 26 C C24 Y6Y . . . S 3 199.834 139.561 146.235 1 14.83 ? C24 Y6Y 903 C 1 
HETATM 27 C C25 Y6Y . . . S 3 200.106 140.4 147.301 1 14.83 ? C25 Y6Y 903 C 1 
HETATM 28 C C26 Y6Y . . . S 3 200.096 139.886 148.588 1 14.83 ? C26 Y6Y 903 C 1 
HETATM 29 C C4 Y6Y . . . S 3 203.764 141.44 149.773 1 14.83 ? C4 Y6Y 903 C 1 
HETATM 30 C C7 Y6Y . . . S 3 207.336 142.023 148.743 1 14.83 ? C7 Y6Y 903 C 1 
HETATM 31 N N2 Y6Y . . . S 3 199.816 138.022 150.08 1 14.83 ? N2 Y6Y 903 C 1 
HETATM 32 N N3 Y6Y . . . S 3 199.572 138.276 146.469 1 14.83 ? N3 Y6Y 903 C 1 
HETATM 33 O O1 Y6Y . . . S 3 210.557 145.443 146.918 1 14.83 ? O1 Y6Y 903 C 1 
HETATM 34 O O2 Y6Y . . . S 3 202.517 139.508 150.385 1 14.83 ? O2 Y6Y 903 C 1 
HETATM 35 S S Y6Y . . . S 3 210.939 144.222 147.568 1 14.83 ? S Y6Y 903 C 1 
HETATM 36 S S1 Y6Y . . . S 3 197.1 137.742 150.083 1 14.83 ? S1 Y6Y 903 C 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    51 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           36 
#