data_7KVP
#
_model_server_result.job_id            OevdJPKLisxqGsYVHCdgRw 
_model_server_result.datetime_utc      '2024-10-11 02:21:17' 
_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          7kvp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    7KVP 
#
_exptl.entry_id    7KVP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              583.783 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'tert-butyl [(2R)-1-(naphthalen-1-yl)-3-{[(2S)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate' 
_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            7KVP 
_cell.length_a            78.19 
_cell.length_b            102.34 
_cell.length_c            128.3 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KVP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N30 X6J . A X6J 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
#
_chem_comp.formula           'C35 H41 N3 O3 S' 
_chem_comp.formula_weight    583.783 
_chem_comp.id                X6J 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'tert-butyl [(2R)-1-(naphthalen-1-yl)-3-{[(2S)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate' 
_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
C40 C39 X6J doub 458 n y 
C40 C41 X6J sing 459 n y 
C39 C38 X6J sing 460 n y 
C41 C42 X6J doub 461 n y 
C04 C02 X6J sing 462 n n 
C38 C37 X6J doub 463 n y 
O07 C06 X6J doub 464 n n 
C42 C37 X6J sing 465 n y 
C42 C33 X6J sing 466 n y 
N08 C06 X6J sing 467 n n 
N08 C09 X6J sing 468 n n 
C03 C02 X6J sing 469 n n 
C29 C28 X6J doub 470 n y 
C29 N30 X6J sing 471 n y 
C28 C27 X6J sing 472 n y 
C06 O05 X6J sing 473 n n 
C32 C33 X6J sing 474 n n 
C32 C09 X6J sing 475 n n 
C37 C36 X6J sing 476 n y 
C02 O05 X6J sing 477 n n 
C02 C01 X6J sing 478 n n 
C33 C34 X6J doub 479 n y 
C09 C10 X6J sing 480 n n 
N30 C31 X6J doub 481 n y 
C27 C26 X6J doub 482 n y 
C36 C35 X6J doub 483 n y 
C34 C35 X6J sing 484 n y 
S11 C10 X6J sing 485 n n 
S11 C12 X6J sing 486 n n 
C31 C26 X6J sing 487 n y 
C26 C25 X6J sing 488 n n 
C13 C12 X6J sing 489 n n 
C13 C14 X6J sing 490 n n 
C12 C20 X6J sing 491 n n 
C25 C24 X6J sing 492 n n 
N22 C20 X6J sing 493 n n 
N22 C23 X6J sing 494 n n 
C20 O21 X6J doub 495 n n 
C24 C23 X6J sing 496 n n 
C14 C15 X6J doub 497 n y 
C14 C19 X6J sing 498 n y 
C15 C16 X6J sing 499 n y 
C19 C18 X6J doub 500 n y 
C16 C17 X6J doub 501 n y 
C18 C17 X6J sing 502 n y 
C10 H1 X6J sing 503 n n 
C10 H2 X6J sing 504 n n 
C01 H3 X6J sing 505 n n 
C01 H4 X6J sing 506 n n 
C01 H5 X6J sing 507 n n 
C03 H6 X6J sing 508 n n 
C03 H7 X6J sing 509 n n 
C03 H8 X6J sing 510 n n 
C04 H9 X6J sing 511 n n 
C04 H10 X6J sing 512 n n 
C04 H11 X6J sing 513 n n 
C09 H12 X6J sing 514 n n 
C12 H13 X6J sing 515 n n 
C13 H14 X6J sing 516 n n 
C13 H15 X6J sing 517 n n 
C15 H16 X6J sing 518 n n 
C16 H17 X6J sing 519 n n 
C17 H18 X6J sing 520 n n 
C18 H19 X6J sing 521 n n 
C19 H20 X6J sing 522 n n 
C23 H21 X6J sing 523 n n 
C23 H22 X6J sing 524 n n 
C24 H23 X6J sing 525 n n 
C24 H24 X6J sing 526 n n 
C25 H25 X6J sing 527 n n 
C25 H26 X6J sing 528 n n 
C27 H27 X6J sing 529 n n 
C28 H28 X6J sing 530 n n 
C29 H29 X6J sing 531 n n 
C31 H30 X6J sing 532 n n 
C32 H31 X6J sing 533 n n 
C32 H32 X6J sing 534 n n 
C34 H33 X6J sing 535 n n 
C35 H34 X6J sing 536 n n 
C36 H35 X6J sing 537 n n 
C38 H36 X6J sing 538 n n 
C39 H37 X6J sing 539 n n 
C40 H38 X6J sing 540 n n 
C41 H39 X6J sing 541 n n 
N08 H40 X6J sing 542 n n 
N22 H41 X6J sing 543 n n 
#
_atom_sites.entry_id                     7KVP 
_atom_sites.fract_transf_matrix[1][1]    0.012789 
_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]    0.009771 
_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]    0.007794 
_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 HEM A 1 601 500 HEM HEM . 
C 3 X6J A 1 602 700 X6J 381 . 
D 4 HOH A 1 701 2 HOH HOH . 
D 4 HOH A 2 702 1 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 X6J . . . C 3 -23.377 -15.12 -9.13 1 266.14 ? C10 X6J 602 A 1 
HETATM 2 C C01 X6J . . . C 3 -25.629 -10.47 -9.774 1 146.62 ? C01 X6J 602 A 1 
HETATM 3 C C02 X6J . . . C 3 -24.891 -11.343 -10.806 1 164.66 ? C02 X6J 602 A 1 
HETATM 4 C C03 X6J . . . C 3 -25.834 -12.441 -11.248 1 156.34 ? C03 X6J 602 A 1 
HETATM 5 C C04 X6J . . . C 3 -24.557 -10.535 -12.049 1 169.04 ? C04 X6J 602 A 1 
HETATM 6 C C06 X6J . . . C 3 -22.833 -12.634 -11.093 1 218.97 ? C06 X6J 602 A 1 
HETATM 7 C C09 X6J . . . C 3 -22.423 -14.968 -10.291 1 229.4 ? C09 X6J 602 A 1 
HETATM 8 C C12 X6J . . . C 3 -24.299 -17.427 -7.77 1 243.99 ? C12 X6J 602 A 1 
HETATM 9 C C13 X6J . . . C 3 -25.145 -18.66 -7.999 1 219.87 ? C13 X6J 602 A 1 
HETATM 10 C C14 X6J . . . C 3 -25.045 -19.387 -6.685 1 187.31 ? C14 X6J 602 A 1 
HETATM 11 C C15 X6J . . . C 3 -24.964 -20.761 -6.674 1 176 ? C15 X6J 602 A 1 
HETATM 12 C C16 X6J . . . C 3 -24.849 -21.369 -5.448 1 159.92 ? C16 X6J 602 A 1 
HETATM 13 C C17 X6J . . . C 3 -24.812 -20.625 -4.286 1 150.13 ? C17 X6J 602 A 1 
HETATM 14 C C18 X6J . . . C 3 -24.873 -19.247 -4.301 1 149.33 ? C18 X6J 602 A 1 
HETATM 15 C C19 X6J . . . C 3 -25.004 -18.629 -5.512 1 162.71 ? C19 X6J 602 A 1 
HETATM 16 C C20 X6J . . . C 3 -22.851 -17.694 -7.284 1 207.09 ? C20 X6J 602 A 1 
HETATM 17 C C23 X6J . . . C 3 -20.816 -18.932 -6.896 1 146.49 ? C23 X6J 602 A 1 
HETATM 18 C C24 X6J . . . C 3 -19.951 -20.143 -7.214 1 106.68 ? C24 X6J 602 A 1 
HETATM 19 C C25 X6J . . . C 3 -20.806 -21.286 -7.737 1 88.19 ? C25 X6J 602 A 1 
HETATM 20 C C26 X6J . . . C 3 -20.16 -21.897 -8.968 1 101.04 ? C26 X6J 602 A 1 
HETATM 21 C C27 X6J . . . C 3 -20.982 -22.229 -10.016 1 107.04 ? C27 X6J 602 A 1 
HETATM 22 C C28 X6J . . . C 3 -20.415 -22.777 -11.138 1 101.67 ? C28 X6J 602 A 1 
HETATM 23 C C29 X6J . . . C 3 -19.043 -22.981 -11.171 1 93.68 ? C29 X6J 602 A 1 
HETATM 24 C C31 X6J . . . C 3 -18.788 -22.111 -9.06 1 102.64 ? C31 X6J 602 A 1 
HETATM 25 C C32 X6J . . . C 3 -22.189 -16.318 -10.966 1 186.25 ? C32 X6J 602 A 1 
HETATM 26 C C33 X6J . . . C 3 -20.866 -16.942 -10.516 1 140.92 ? C33 X6J 602 A 1 
HETATM 27 C C34 X6J . . . C 3 -20.15 -16.477 -9.411 1 132.07 ? C34 X6J 602 A 1 
HETATM 28 C C35 X6J . . . C 3 -18.944 -17.103 -9.067 1 130.44 ? C35 X6J 602 A 1 
HETATM 29 C C36 X6J . . . C 3 -18.467 -18.177 -9.815 1 132.32 ? C36 X6J 602 A 1 
HETATM 30 C C37 X6J . . . C 3 -19.217 -18.635 -10.944 1 136.22 ? C37 X6J 602 A 1 
HETATM 31 C C38 X6J . . . C 3 -18.777 -19.723 -11.741 1 154.02 ? C38 X6J 602 A 1 
HETATM 32 C C39 X6J . . . C 3 -19.527 -20.144 -12.841 1 156.19 ? C39 X6J 602 A 1 
HETATM 33 C C40 X6J . . . C 3 -20.729 -19.511 -13.166 1 141.26 ? C40 X6J 602 A 1 
HETATM 34 C C41 X6J . . . C 3 -21.163 -18.448 -12.392 1 126.84 ? C41 X6J 602 A 1 
HETATM 35 C C42 X6J . . . C 3 -20.387 -18.023 -11.277 1 123.69 ? C42 X6J 602 A 1 
HETATM 36 N N08 X6J . . . C 3 -23.037 -14.08 -11.261 1 230.64 ? N08 X6J 602 A 1 
HETATM 37 N N22 X6J . . . C 3 -22.161 -18.967 -7.466 1 179.08 ? N22 X6J 602 A 1 
HETATM 38 N N30 X6J . . . C 3 -18.279 -22.644 -10.153 1 85.56 ? N30 X6J 602 A 1 
HETATM 39 O O05 X6J . . . C 3 -23.7 -11.897 -10.227 1 192.98 ? O05 X6J 602 A 1 
HETATM 40 O O07 X6J . . . C 3 -21.951 -12.106 -11.684 1 231.01 ? O07 X6J 602 A 1 
HETATM 41 O O21 X6J . . . C 3 -22.266 -16.846 -6.698 1 196.6 ? O21 X6J 602 A 1 
HETATM 42 S S11 X6J . . . C 3 -24.229 -16.69 -9.392 1 309.62 ? S11 X6J 602 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           42 
#