data_3VSX
#
_model_server_result.job_id            nJKNCuznZnyjYYYTCiEEgQ 
_model_server_result.datetime_utc      '2024-11-22 08:18:45' 
_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          3vsx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":402}' 
#
_entry.id    3VSX 
#
_exptl.entry_id    3VSX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              524.096 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide 
_entity.pdbx_number_of_molecules    2 
_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            3VSX 
_cell.length_a            138.188 
_cell.length_b            138.188 
_cell.length_c            138.188 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VSX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
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 
PISA hexameric 6 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D 1 1 
B,E,F 2 1 
A,B,C,D,E,F 3 1,2,3 
#
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' 6_533 z+1/2,-x-3/2,-y-2 0 0 1 -1 0 0 0 -1 0 69.094 -207.282 -276.376 
3 'crystal symmetry operation' 12_334 -y-3/2,-z-2,x-1/2 0 -1 0 0 0 -1 1 0 0 -207.282 -276.376 -69.094 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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
disulf ? disulf1 A SG CYS 51 A CYS 51 1_555 A SG CYS 58 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? 
disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? 
disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? 
disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? 
covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? 
covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
#
_chem_comp.formula           'C26 H42 Cl N5 O4' 
_chem_comp.formula_weight    524.096 
_chem_comp.id                R32 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-2-(propan-2-yl)hexanamide 
_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
N35 C32 R32 sing 305 n n 
O36 C32 R32 doub 306 n n 
C32 C25 R32 sing 307 n n 
C33 C25 R32 sing 308 n n 
C25 C34 R32 sing 309 n n 
C25 C24 R32 sing 310 n n 
C24 N23 R32 sing 311 n n 
N23 C22 R32 sing 312 n n 
O27 C19 R32 sing 313 n n 
C15 C10 R32 sing 314 n n 
C22 C21 R32 sing 315 n n 
C22 O29 R32 doub 316 n n 
C19 C18 R32 sing 317 n n 
C19 C20 R32 sing 318 n n 
C31 C28 R32 sing 319 n n 
C21 C28 R32 sing 320 n n 
C21 C20 R32 sing 321 n n 
C17 C18 R32 sing 322 n n 
C17 N11 R32 sing 323 n n 
C16 C10 R32 sing 324 n n 
C10 N11 R32 sing 325 n n 
C10 C9 R32 sing 326 n n 
N26 C18 R32 sing 327 n n 
C28 C30 R32 sing 328 n n 
N11 C12 R32 sing 329 n n 
C9 N7 R32 sing 330 n n 
C12 C13 R32 sing 331 n n 
N7 C13 R32 sing 332 n n 
N7 C2 R32 sing 333 n n 
C13 O14 R32 doub 334 n n 
CL1 C3 R32 sing 335 n n 
C2 C3 R32 doub 336 n y 
C2 C1 R32 sing 337 n y 
C3 C4 R32 sing 338 n y 
C1 C6 R32 doub 339 n y 
C4 C5 R32 doub 340 n y 
C6 C5 R32 sing 341 n y 
C1 H1 R32 sing 342 n n 
C4 H2 R32 sing 343 n n 
C5 H3 R32 sing 344 n n 
C6 H4 R32 sing 345 n n 
C9 H5 R32 sing 346 n n 
C9 H6 R32 sing 347 n n 
C12 H8 R32 sing 348 n n 
C12 H9 R32 sing 349 n n 
C15 H10 R32 sing 350 n n 
C15 H11 R32 sing 351 n n 
C15 H12 R32 sing 352 n n 
C16 H13 R32 sing 353 n n 
C16 H14 R32 sing 354 n n 
C16 H15 R32 sing 355 n n 
C17 H16 R32 sing 356 n n 
C17 H17 R32 sing 357 n n 
C18 H18 R32 sing 358 n n 
C19 H19 R32 sing 359 n n 
C20 H20 R32 sing 360 n n 
C20 H21 R32 sing 361 n n 
C21 H22 R32 sing 362 n n 
N23 H23 R32 sing 363 n n 
C24 H24 R32 sing 364 n n 
C24 H25 R32 sing 365 n n 
N26 H26 R32 sing 366 n n 
N26 H27 R32 sing 367 n n 
O27 H29 R32 sing 368 n n 
C28 H30 R32 sing 369 n n 
C30 H31 R32 sing 370 n n 
C30 H32 R32 sing 371 n n 
C30 H33 R32 sing 372 n n 
C31 H34 R32 sing 373 n n 
C31 H35 R32 sing 374 n n 
C31 H36 R32 sing 375 n n 
C33 H37 R32 sing 376 n n 
C33 H38 R32 sing 377 n n 
C33 H39 R32 sing 378 n n 
C34 H40 R32 sing 379 n n 
C34 H41 R32 sing 380 n n 
C34 H42 R32 sing 381 n n 
N35 H43 R32 sing 382 n n 
N35 H44 R32 sing 383 n n 
#
_atom_sites.entry_id                     3VSX 
_atom_sites.fract_transf_matrix[1][1]    0.007237 
_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]    0.007237 
_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]    0.007237 
_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
C 2 NAG A 1 401 401 NAG NAG . 
D 3 R32 A 1 402 501 R32 R32 . 
E 2 NAG B 1 401 401 NAG NAG . 
F 3 R32 B 1 402 501 R32 R32 . 
#
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 R32 . . . F 3 -39.547 -189.756 -118.665 1 43.26 ? C1 R32 402 B 1 
HETATM 2 C C2 R32 . . . F 3 -40.185 -190.93 -118.28 1 42.2 ? C2 R32 402 B 1 
HETATM 3 C C3 R32 . . . F 3 -41.232 -190.858 -117.369 1 43.23 ? C3 R32 402 B 1 
HETATM 4 C C4 R32 . . . F 3 -41.66 -189.655 -116.833 1 43.4 ? C4 R32 402 B 1 
HETATM 5 C C5 R32 . . . F 3 -41.02 -188.485 -117.22 1 43.22 ? C5 R32 402 B 1 
HETATM 6 C C6 R32 . . . F 3 -39.966 -188.534 -118.134 1 43.99 ? C6 R32 402 B 1 
HETATM 7 N N7 R32 . . . F 3 -39.74 -192.124 -118.832 1 39.08 ? N7 R32 402 B 1 
HETATM 8 CL CL1 R32 . . . F 3 -42.029 -192.315 -116.885 1 46.04 ? CL1 R32 402 B 1 
HETATM 9 C C9 R32 . . . F 3 -40.042 -192.403 -120.254 1 36.85 ? C9 R32 402 B 1 
HETATM 10 C C10 R32 . . . F 3 -39.899 -193.861 -120.672 1 36.33 ? C10 R32 402 B 1 
HETATM 11 N N11 R32 . . . F 3 -38.658 -194.342 -120.12 1 34.79 ? N11 R32 402 B 1 
HETATM 12 C C12 R32 . . . F 3 -38.556 -194.317 -118.679 1 35.37 ? C12 R32 402 B 1 
HETATM 13 C C13 R32 . . . F 3 -39.035 -193.002 -118.032 1 37.37 ? C13 R32 402 B 1 
HETATM 14 O O14 R32 . . . F 3 -38.787 -192.77 -116.854 1 36.28 ? O14 R32 402 B 1 
HETATM 15 C C15 R32 . . . F 3 -39.873 -193.967 -122.2 1 35.72 ? C15 R32 402 B 1 
HETATM 16 C C16 R32 . . . F 3 -41.067 -194.688 -120.125 1 36.37 ? C16 R32 402 B 1 
HETATM 17 C C17 R32 . . . F 3 -38.013 -195.45 -120.798 1 34.15 ? C17 R32 402 B 1 
HETATM 18 C C18 R32 . . . F 3 -36.499 -195.413 -120.633 1 33.39 ? C18 R32 402 B 1 
HETATM 19 C C19 R32 . . . F 3 -35.852 -196.753 -120.986 1 31.83 ? C19 R32 402 B 1 
HETATM 20 C C20 R32 . . . F 3 -34.434 -196.908 -120.424 1 30 ? C20 R32 402 B 1 
HETATM 21 C C21 R32 . . . F 3 -33.78 -198.239 -120.829 1 26.71 ? C21 R32 402 B 1 
HETATM 22 C C22 R32 . . . F 3 -34.603 -199.408 -120.282 1 27.98 ? C22 R32 402 B 1 
HETATM 23 N N23 R32 . . . F 3 -35.009 -200.268 -121.238 1 27.96 ? N23 R32 402 B 1 
HETATM 24 C C24 R32 . . . F 3 -35.805 -201.412 -120.811 1 29.55 ? C24 R32 402 B 1 
HETATM 25 C C25 R32 . . . F 3 -35.131 -202.732 -121.218 1 30.47 ? C25 R32 402 B 1 
HETATM 26 N N26 R32 . . . F 3 -35.898 -194.287 -121.338 1 34.43 ? N26 R32 402 B 1 
HETATM 27 O O27 R32 . . . F 3 -35.87 -196.965 -122.377 1 30.66 ? O27 R32 402 B 1 
HETATM 28 C C28 R32 . . . F 3 -32.327 -198.354 -120.365 1 22.6 ? C28 R32 402 B 1 
HETATM 29 O O29 R32 . . . F 3 -34.85 -199.513 -119.086 1 29.23 ? O29 R32 402 B 1 
HETATM 30 C C30 R32 . . . F 3 -31.506 -197.111 -120.685 1 19.99 ? C30 R32 402 B 1 
HETATM 31 C C31 R32 . . . F 3 -31.651 -199.638 -120.844 1 22.19 ? C31 R32 402 B 1 
HETATM 32 C C32 R32 . . . F 3 -35.006 -202.754 -122.743 1 32.22 ? C32 R32 402 B 1 
HETATM 33 C C33 R32 . . . F 3 -35.99 -203.927 -120.81 1 30.48 ? C33 R32 402 B 1 
HETATM 34 C C34 R32 . . . F 3 -33.733 -202.848 -120.611 1 28.09 ? C34 R32 402 B 1 
HETATM 35 N N35 R32 . . . F 3 -36.196 -202.641 -123.372 1 34.2 ? N35 R32 402 B 1 
HETATM 36 O O36 R32 . . . F 3 -33.922 -202.867 -123.301 1 33.89 ? O36 R32 402 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           475 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#