data_8J37
#
_model_server_result.job_id            kMDTJ3_D52aQCSJzKy55qw 
_model_server_result.datetime_utc      '2024-11-20 01:26:01' 
_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          8j37 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8J37 
#
_exptl.entry_id    8J37 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              474.55 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide 
_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          108.709 
_cell.angle_gamma         90 
_cell.entry_id            8J37 
_cell.length_a            55.628 
_cell.length_b            98.98 
_cell.length_c            59.56 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8J37 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D 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
covale ? covale1 A SG CYS 143 A CYS 145 1_555 C C34 V2M . A V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? 
covale ? covale2 B SG CYS 143 B CYS 145 1_555 D C34 V2M . B V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? 
#
_chem_comp.formula           'C24 H34 N4 O6' 
_chem_comp.formula_weight    474.55 
_chem_comp.id                V2M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form' 
#
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
O37 C36 V2M sing 358 n n 
C36 C34 V2M sing 359 n n 
O35 C34 V2M sing 360 n n 
C20 C18 V2M sing 361 n n 
C34 C24 V2M sing 362 n n 
O22 C21 V2M doub 363 n n 
C17 C18 V2M sing 364 n n 
C17 C15 V2M sing 365 n n 
C18 C19 V2M sing 366 n n 
C24 N23 V2M sing 367 n n 
C24 C26 V2M sing 368 n n 
C21 N23 V2M sing 369 n n 
C21 C15 V2M sing 370 n n 
C1 O2 V2M sing 371 n n 
C15 N14 V2M sing 372 n n 
C29 C30 V2M sing 373 n n 
C29 C27 V2M sing 374 n n 
O2 C3 V2M sing 375 n n 
N14 C12 V2M sing 376 n n 
C26 C27 V2M sing 377 n n 
C10 C11 V2M sing 378 n y 
C10 C9 V2M doub 379 n y 
C30 N31 V2M sing 380 n n 
C27 C32 V2M sing 381 n n 
C3 C11 V2M doub 382 n y 
C3 C4 V2M sing 383 n y 
C12 C9 V2M sing 384 n n 
C12 O13 V2M doub 385 n n 
C11 C7 V2M sing 386 n y 
C9 N8 V2M sing 387 n y 
C4 C5 V2M doub 388 n y 
N31 C32 V2M sing 389 n n 
C32 O33 V2M doub 390 n n 
C7 N8 V2M sing 391 n y 
C7 C6 V2M doub 392 n y 
C5 C6 V2M sing 393 n y 
C1 H1 V2M sing 394 n n 
C1 H2 V2M sing 395 n n 
C1 H3 V2M sing 396 n n 
C4 H4 V2M sing 397 n n 
C5 H5 V2M sing 398 n n 
C6 H6 V2M sing 399 n n 
N8 H7 V2M sing 400 n n 
C10 H8 V2M sing 401 n n 
N14 H9 V2M sing 402 n n 
C15 H10 V2M sing 403 n n 
C17 H11 V2M sing 404 n n 
C17 H12 V2M sing 405 n n 
C18 H13 V2M sing 406 n n 
C19 H14 V2M sing 407 n n 
C19 H15 V2M sing 408 n n 
C19 H16 V2M sing 409 n n 
C20 H17 V2M sing 410 n n 
C20 H18 V2M sing 411 n n 
C20 H19 V2M sing 412 n n 
N23 H20 V2M sing 413 n n 
C24 H21 V2M sing 414 n n 
C26 H22 V2M sing 415 n n 
C26 H23 V2M sing 416 n n 
C27 H24 V2M sing 417 n n 
C29 H25 V2M sing 418 n n 
C29 H26 V2M sing 419 n n 
C30 H27 V2M sing 420 n n 
C30 H28 V2M sing 421 n n 
N31 H29 V2M sing 422 n n 
C34 H30 V2M sing 423 n n 
O35 H31 V2M sing 424 n n 
C36 H32 V2M sing 425 n n 
C36 H33 V2M sing 426 n n 
O37 H34 V2M sing 427 n n 
#
_atom_sites.entry_id                     8J37 
_atom_sites.fract_transf_matrix[1][1]    0.017977 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.006088 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010103 
_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]    0.017726 
_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 V2M A 1 401 401 V2M V2M . 
D 2 V2M B 1 401 401 V2M V2M . 
E 3 HOH A 1 501 70 HOH HOH . 
E 3 HOH A 2 502 71 HOH HOH . 
E 3 HOH A 3 503 98 HOH HOH . 
E 3 HOH A 4 504 40 HOH HOH . 
E 3 HOH A 5 505 88 HOH HOH . 
E 3 HOH A 6 506 31 HOH HOH . 
E 3 HOH A 7 507 11 HOH HOH . 
E 3 HOH A 8 508 25 HOH HOH . 
E 3 HOH A 9 509 93 HOH HOH . 
E 3 HOH A 10 510 91 HOH HOH . 
E 3 HOH A 11 511 56 HOH HOH . 
E 3 HOH A 12 512 86 HOH HOH . 
E 3 HOH A 13 513 5 HOH HOH . 
E 3 HOH A 14 514 37 HOH HOH . 
E 3 HOH A 15 515 52 HOH HOH . 
E 3 HOH A 16 516 81 HOH HOH . 
E 3 HOH A 17 517 85 HOH HOH . 
E 3 HOH A 18 518 80 HOH HOH . 
E 3 HOH A 19 519 18 HOH HOH . 
E 3 HOH A 20 520 20 HOH HOH . 
E 3 HOH A 21 521 10 HOH HOH . 
E 3 HOH A 22 522 32 HOH HOH . 
E 3 HOH A 23 523 72 HOH HOH . 
E 3 HOH A 24 524 76 HOH HOH . 
E 3 HOH A 25 525 46 HOH HOH . 
E 3 HOH A 26 526 59 HOH HOH . 
E 3 HOH A 27 527 90 HOH HOH . 
E 3 HOH A 28 528 19 HOH HOH . 
E 3 HOH A 29 529 102 HOH HOH . 
E 3 HOH A 30 530 38 HOH HOH . 
E 3 HOH A 31 531 12 HOH HOH . 
E 3 HOH A 32 532 34 HOH HOH . 
E 3 HOH A 33 533 35 HOH HOH . 
E 3 HOH A 34 534 1 HOH HOH . 
E 3 HOH A 35 535 67 HOH HOH . 
E 3 HOH A 36 536 9 HOH HOH . 
E 3 HOH A 37 537 78 HOH HOH . 
E 3 HOH A 38 538 26 HOH HOH . 
E 3 HOH A 39 539 16 HOH HOH . 
E 3 HOH A 40 540 69 HOH HOH . 
E 3 HOH A 41 541 75 HOH HOH . 
E 3 HOH A 42 542 77 HOH HOH . 
E 3 HOH A 43 543 89 HOH HOH . 
E 3 HOH A 44 544 74 HOH HOH . 
E 3 HOH A 45 545 101 HOH HOH . 
E 3 HOH A 46 546 51 HOH HOH . 
E 3 HOH A 47 547 82 HOH HOH . 
E 3 HOH A 48 548 49 HOH HOH . 
E 3 HOH A 49 549 57 HOH HOH . 
E 3 HOH A 50 550 68 HOH HOH . 
E 3 HOH A 51 551 66 HOH HOH . 
E 3 HOH A 52 552 22 HOH HOH . 
E 3 HOH A 53 553 61 HOH HOH . 
E 3 HOH A 54 554 105 HOH HOH . 
E 3 HOH A 55 555 83 HOH HOH . 
E 3 HOH A 56 556 63 HOH HOH . 
E 3 HOH A 57 557 84 HOH HOH . 
E 3 HOH A 58 558 97 HOH HOH . 
E 3 HOH A 59 559 99 HOH HOH . 
E 3 HOH A 60 560 103 HOH HOH . 
F 3 HOH B 1 501 45 HOH HOH . 
F 3 HOH B 2 502 65 HOH HOH . 
F 3 HOH B 3 503 62 HOH HOH . 
F 3 HOH B 4 504 73 HOH HOH . 
F 3 HOH B 5 505 8 HOH HOH . 
F 3 HOH B 6 506 50 HOH HOH . 
F 3 HOH B 7 507 54 HOH HOH . 
F 3 HOH B 8 508 55 HOH HOH . 
F 3 HOH B 9 509 7 HOH HOH . 
F 3 HOH B 10 510 6 HOH HOH . 
F 3 HOH B 11 511 4 HOH HOH . 
F 3 HOH B 12 512 87 HOH HOH . 
F 3 HOH B 13 513 43 HOH HOH . 
F 3 HOH B 14 514 36 HOH HOH . 
F 3 HOH B 15 515 96 HOH HOH . 
F 3 HOH B 16 516 14 HOH HOH . 
F 3 HOH B 17 517 21 HOH HOH . 
F 3 HOH B 18 518 15 HOH HOH . 
F 3 HOH B 19 519 53 HOH HOH . 
F 3 HOH B 20 520 64 HOH HOH . 
F 3 HOH B 21 521 28 HOH HOH . 
F 3 HOH B 22 522 17 HOH HOH . 
F 3 HOH B 23 523 33 HOH HOH . 
F 3 HOH B 24 524 3 HOH HOH . 
F 3 HOH B 25 525 60 HOH HOH . 
F 3 HOH B 26 526 2 HOH HOH . 
F 3 HOH B 27 527 48 HOH HOH . 
F 3 HOH B 28 528 29 HOH HOH . 
F 3 HOH B 29 529 58 HOH HOH . 
F 3 HOH B 30 530 95 HOH HOH . 
F 3 HOH B 31 531 94 HOH HOH . 
F 3 HOH B 32 532 42 HOH HOH . 
F 3 HOH B 33 533 30 HOH HOH . 
F 3 HOH B 34 534 41 HOH HOH . 
F 3 HOH B 35 535 39 HOH HOH . 
F 3 HOH B 36 536 13 HOH HOH . 
F 3 HOH B 37 537 92 HOH HOH . 
F 3 HOH B 38 538 100 HOH HOH . 
F 3 HOH B 39 539 47 HOH HOH . 
F 3 HOH B 40 540 44 HOH HOH . 
F 3 HOH B 41 541 27 HOH HOH . 
F 3 HOH B 42 542 24 HOH HOH . 
F 3 HOH B 43 543 79 HOH HOH . 
F 3 HOH B 44 544 104 HOH HOH . 
F 3 HOH B 45 545 23 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 V2M . . . C 2 -24.321 -10.505 -4.228 1 34.68 ? C1 V2M 401 A 1 
HETATM 2 O O2 V2M . . . C 2 -23.754 -10.309 -2.94 1 32.55 ? O2 V2M 401 A 1 
HETATM 3 C C3 V2M . . . C 2 -23.132 -9.123 -2.691 1 34.2 ? C3 V2M 401 A 1 
HETATM 4 C C4 V2M . . . C 2 -23.1 -8.079 -3.585 1 29.99 ? C4 V2M 401 A 1 
HETATM 5 C C5 V2M . . . C 2 -22.438 -6.89 -3.259 1 33.02 ? C5 V2M 401 A 1 
HETATM 6 C C6 V2M . . . C 2 -21.812 -6.711 -2.058 1 32.38 ? C6 V2M 401 A 1 
HETATM 7 C C7 V2M . . . C 2 -21.849 -7.762 -1.148 1 32.25 ? C7 V2M 401 A 1 
HETATM 8 N N8 V2M . . . C 2 -21.323 -7.868 0.107 1 30.64 ? N8 V2M 401 A 1 
HETATM 9 C C9 V2M . . . C 2 -21.621 -9.111 0.613 1 29.17 ? C9 V2M 401 A 1 
HETATM 10 C C10 V2M . . . C 2 -22.341 -9.815 -0.316 1 29.43 ? C10 V2M 401 A 1 
HETATM 11 C C11 V2M . . . C 2 -22.501 -8.976 -1.449 1 30.74 ? C11 V2M 401 A 1 
HETATM 12 C C12 V2M . . . C 2 -21.143 -9.468 1.952 1 29.61 ? C12 V2M 401 A 1 
HETATM 13 O O13 V2M . . . C 2 -20.5 -8.676 2.633 1 29.52 ? O13 V2M 401 A 1 
HETATM 14 N N14 V2M . . . C 2 -21.44 -10.7 2.374 1 28.63 ? N14 V2M 401 A 1 
HETATM 15 C C15 V2M . . . C 2 -20.901 -11.198 3.625 1 26.13 ? C15 V2M 401 A 1 
HETATM 16 C C17 V2M . . . C 2 -21.585 -12.505 4.016 1 26.21 ? C17 V2M 401 A 1 
HETATM 17 C C18 V2M . . . C 2 -23.067 -12.37 4.349 1 28 ? C18 V2M 401 A 1 
HETATM 18 C C19 V2M . . . C 2 -23.699 -13.727 4.598 1 26.41 ? C19 V2M 401 A 1 
HETATM 19 C C20 V2M . . . C 2 -23.282 -11.451 5.537 1 27.31 ? C20 V2M 401 A 1 
HETATM 20 C C21 V2M . . . C 2 -19.39 -11.406 3.554 1 30.34 ? C21 V2M 401 A 1 
HETATM 21 O O22 V2M . . . C 2 -18.881 -11.932 2.573 1 29.44 ? O22 V2M 401 A 1 
HETATM 22 N N23 V2M . . . C 2 -18.683 -11.058 4.632 1 25.16 ? N23 V2M 401 A 1 
HETATM 23 C C24 V2M . . . C 2 -17.256 -11.304 4.68 1 28.82 ? C24 V2M 401 A 1 
HETATM 24 C C26 V2M . . . C 2 -16.482 -10.013 4.952 1 27.26 ? C26 V2M 401 A 1 
HETATM 25 C C27 V2M . . . C 2 -16.369 -9.206 3.66 1 31.06 ? C27 V2M 401 A 1 
HETATM 26 C C29 V2M . . . C 2 -15.541 -9.898 2.589 1 27.41 ? C29 V2M 401 A 1 
HETATM 27 C C30 V2M . . . C 2 -14.84 -8.775 1.848 1 29.1 ? C30 V2M 401 A 1 
HETATM 28 N N31 V2M . . . C 2 -14.842 -7.686 2.816 1 30.6 ? N31 V2M 401 A 1 
HETATM 29 C C32 V2M . . . C 2 -15.685 -7.861 3.818 1 29.31 ? C32 V2M 401 A 1 
HETATM 30 O O33 V2M . . . C 2 -15.918 -7.045 4.705 1 24.96 ? O33 V2M 401 A 1 
HETATM 31 C C34 V2M . . . C 2 -17.057 -12.292 5.916 1 30.97 ? C34 V2M 401 A 1 
HETATM 32 O O35 V2M . . . C 2 -15.889 -12.421 6.276 1 27.48 ? O35 V2M 401 A 1 
HETATM 33 C C36 V2M . . . C 2 -17.901 -13.537 5.772 1 28.41 ? C36 V2M 401 A 1 
HETATM 34 O O37 V2M . . . C 2 -17.504 -14.582 6.626 1 28.81 ? O37 V2M 401 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           34 
#