data_1W12 # _model_server_result.job_id ZpTy050g_C5JIM-2TSFxmg _model_server_result.datetime_utc '2025-02-05 11:57:25' _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 1w12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1245}' # _entry.id 1W12 # _exptl.entry_id 1W12 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.692 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-((1S)-4-{[AMINO(IMINO)METHYL]AMINO}-1-FORMYLBUTYL)-2-{(3R)-3-[(BENZYLSULFONYL)AMINO]-2-OXO-5-PHENYL-2,3-DIHYDRO-1H-1,4-BENZODIAZEPIN-1-YL}ACETAMIDE _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 1W12 _cell.length_a 55.006 _cell.length_b 55.006 _cell.length_c 151.609 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1W12 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 31 U CYS 42 1_555 A SG CYS 47 U CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 39 U CYS 50 1_555 A SG CYS 110 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 135 U CYS 136 1_555 A SG CYS 204 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf4 A SG CYS 167 U CYS 168 1_555 A SG CYS 183 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 194 U CYS 191 1_555 A SG CYS 222 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A OG SER 198 U SER 195 1_555 B C6 SL1 . U SL1 1245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? # _chem_comp.formula 'C30 H33 N7 O5 S' _chem_comp.formula_weight 603.692 _chem_comp.id SL1 _chem_comp.mon_nstd_flag . _chem_comp.name N-((1S)-4-{[AMINO(IMINO)METHYL]AMINO}-1-FORMYLBUTYL)-2-{(3R)-3-[(BENZYLSULFONYL)AMINO]-2-OXO-5-PHENYL-2,3-DIHYDRO-1H-1,4-BENZODIAZEPIN-1-YL}ACETAMIDE _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 N1 C1 SL1 sing 290 n n N1 S SL1 sing 291 n n N1 H1 SL1 sing 292 n n C1 C2 SL1 sing 293 n n C1 N4 SL1 sing 294 n n C1 HA SL1 sing 295 n n C2 O1 SL1 doub 296 n n C2 N2 SL1 sing 297 n n N2 C3 SL1 sing 298 n n N2 C7 SL1 sing 299 n n C3 C4 SL1 sing 300 n n C3 H3C1 SL1 sing 301 n n C3 H3C2 SL1 sing 302 n n C4 O3 SL1 doub 303 n n C4 N3 SL1 sing 304 n n N3 C5 SL1 sing 305 n n N3 H3 SL1 sing 306 n n C5 C6 SL1 sing 307 n n C5 C20 SL1 sing 308 n n C5 H5 SL1 sing 309 n n C6 O2 SL1 doub 310 n n C6 H6 SL1 sing 311 n n C7 C9 SL1 doub 312 n y C7 C19 SL1 sing 313 n y C9 C8 SL1 sing 314 n n C9 C16 SL1 sing 315 n y C8 N4 SL1 doub 316 n n C8 C10 SL1 sing 317 n n C10 C11 SL1 doub 318 n y C10 C15 SL1 sing 319 n y C11 C12 SL1 sing 320 n y C11 H11 SL1 sing 321 n n C12 C13 SL1 doub 322 n y C12 H12 SL1 sing 323 n n C13 C14 SL1 sing 324 n y C13 H13 SL1 sing 325 n n C14 C15 SL1 doub 326 n y C14 H14 SL1 sing 327 n n C15 H15 SL1 sing 328 n n C16 C17 SL1 doub 329 n y C16 H16 SL1 sing 330 n n C17 C18 SL1 sing 331 n y C17 H17 SL1 sing 332 n n C18 C19 SL1 doub 333 n y C18 H18 SL1 sing 334 n n C19 H19 SL1 sing 335 n n C20 C21 SL1 sing 336 n n C20 H201 SL1 sing 337 n n C20 H202 SL1 sing 338 n n C21 C22 SL1 sing 339 n n C21 H211 SL1 sing 340 n n C21 H212 SL1 sing 341 n n C22 N5 SL1 sing 342 n n C22 H221 SL1 sing 343 n n C22 H222 SL1 sing 344 n n N5 C23 SL1 sing 345 n n N5 HB SL1 sing 346 n n C23 N6 SL1 sing 347 n n C23 N7 SL1 doub 348 n n N6 H6N1 SL1 sing 349 n n N6 H6N2 SL1 sing 350 n n N7 H7 SL1 sing 351 n n S O4 SL1 doub 352 n n S O5 SL1 doub 353 n n S C24 SL1 sing 354 n n C24 C25 SL1 sing 355 n n C24 H241 SL1 sing 356 n n C24 H242 SL1 sing 357 n n C25 C26 SL1 doub 358 n y C25 C30 SL1 sing 359 n y C26 C27 SL1 sing 360 n y C26 H26 SL1 sing 361 n n C27 C28 SL1 doub 362 n y C27 H27 SL1 sing 363 n n C28 C29 SL1 sing 364 n y C28 H28 SL1 sing 365 n n C29 C30 SL1 doub 366 n y C29 H29 SL1 sing 367 n n C30 H30 SL1 sing 368 n n # _atom_sites.entry_id 1W12 _atom_sites.fract_transf_matrix[1][1] 0.01818 _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] 0.01818 _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] 0.006596 _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 SL1 U 1 1245 1245 SL1 SL1 . C 3 HOH U 1 2001 2001 HOH HOH . C 3 HOH U 2 2002 2002 HOH HOH . C 3 HOH U 3 2003 2003 HOH HOH . C 3 HOH U 4 2004 2004 HOH HOH . C 3 HOH U 5 2005 2005 HOH HOH . C 3 HOH U 6 2006 2006 HOH HOH . C 3 HOH U 7 2007 2007 HOH HOH . C 3 HOH U 8 2008 2008 HOH HOH . C 3 HOH U 9 2009 2009 HOH HOH . C 3 HOH U 10 2010 2010 HOH HOH . C 3 HOH U 11 2011 2011 HOH HOH . C 3 HOH U 12 2012 2012 HOH HOH . C 3 HOH U 13 2013 2013 HOH HOH . C 3 HOH U 14 2014 2014 HOH HOH . C 3 HOH U 15 2015 2015 HOH HOH . C 3 HOH U 16 2016 2016 HOH HOH . C 3 HOH U 17 2017 2017 HOH HOH . C 3 HOH U 18 2018 2018 HOH HOH . C 3 HOH U 19 2019 2019 HOH HOH . C 3 HOH U 20 2020 2020 HOH HOH . C 3 HOH U 21 2021 2021 HOH HOH . C 3 HOH U 22 2022 2022 HOH HOH . C 3 HOH U 23 2023 2023 HOH HOH . C 3 HOH U 24 2024 2024 HOH HOH . C 3 HOH U 25 2025 2025 HOH HOH . C 3 HOH U 26 2026 2026 HOH HOH . C 3 HOH U 27 2027 2027 HOH HOH . C 3 HOH U 28 2028 2028 HOH HOH . C 3 HOH U 29 2029 2029 HOH HOH . C 3 HOH U 30 2030 2030 HOH HOH . C 3 HOH U 31 2031 2031 HOH HOH . C 3 HOH U 32 2032 2032 HOH HOH . C 3 HOH U 33 2033 2033 HOH HOH . C 3 HOH U 34 2034 2034 HOH HOH . C 3 HOH U 35 2035 2035 HOH HOH . C 3 HOH U 36 2036 2036 HOH HOH . C 3 HOH U 37 2037 2037 HOH HOH . C 3 HOH U 38 2038 2038 HOH HOH . C 3 HOH U 39 2039 2039 HOH HOH . C 3 HOH U 40 2040 2040 HOH HOH . C 3 HOH U 41 2041 2041 HOH HOH . C 3 HOH U 42 2042 2042 HOH HOH . C 3 HOH U 43 2043 2043 HOH HOH . C 3 HOH U 44 2044 2044 HOH HOH . C 3 HOH U 45 2045 2045 HOH HOH . C 3 HOH U 46 2046 2046 HOH HOH . C 3 HOH U 47 2047 2047 HOH HOH . C 3 HOH U 48 2048 2048 HOH HOH . C 3 HOH U 49 2049 2049 HOH HOH . C 3 HOH U 50 2050 2050 HOH HOH . C 3 HOH U 51 2051 2051 HOH HOH . C 3 HOH U 52 2052 2052 HOH HOH . C 3 HOH U 53 2053 2053 HOH HOH . C 3 HOH U 54 2054 2054 HOH HOH . C 3 HOH U 55 2055 2055 HOH HOH . C 3 HOH U 56 2056 2056 HOH HOH . C 3 HOH U 57 2057 2057 HOH HOH . C 3 HOH U 58 2058 2058 HOH HOH . C 3 HOH U 59 2059 2059 HOH HOH . C 3 HOH U 60 2060 2060 HOH HOH . C 3 HOH U 61 2061 2061 HOH HOH . C 3 HOH U 62 2062 2062 HOH HOH . C 3 HOH U 63 2063 2063 HOH HOH . C 3 HOH U 64 2064 2064 HOH HOH . C 3 HOH U 65 2065 2065 HOH HOH . C 3 HOH U 66 2066 2066 HOH HOH . C 3 HOH U 67 2067 2067 HOH HOH . C 3 HOH U 68 2068 2068 HOH HOH . C 3 HOH U 69 2069 2069 HOH HOH . C 3 HOH U 70 2070 2070 HOH HOH . C 3 HOH U 71 2071 2071 HOH HOH . C 3 HOH U 72 2072 2072 HOH HOH . C 3 HOH U 73 2073 2073 HOH HOH . C 3 HOH U 74 2074 2074 HOH HOH . C 3 HOH U 75 2075 2075 HOH HOH . C 3 HOH U 76 2076 2076 HOH HOH . C 3 HOH U 77 2077 2077 HOH HOH . C 3 HOH U 78 2078 2078 HOH HOH . C 3 HOH U 79 2079 2079 HOH HOH . C 3 HOH U 80 2080 2080 HOH HOH . C 3 HOH U 81 2081 2081 HOH HOH . C 3 HOH U 82 2082 2082 HOH HOH . C 3 HOH U 83 2083 2083 HOH HOH . C 3 HOH U 84 2084 2084 HOH HOH . C 3 HOH U 85 2085 2085 HOH HOH . C 3 HOH U 86 2086 2086 HOH HOH . C 3 HOH U 87 2087 2087 HOH HOH . C 3 HOH U 88 2088 2088 HOH HOH . C 3 HOH U 89 2089 2089 HOH HOH . C 3 HOH U 90 2090 2090 HOH HOH . C 3 HOH U 91 2091 2091 HOH HOH . C 3 HOH U 92 2092 2092 HOH HOH . C 3 HOH U 93 2093 2093 HOH HOH . C 3 HOH U 94 2094 2094 HOH HOH . C 3 HOH U 95 2095 2095 HOH HOH . C 3 HOH U 96 2096 2096 HOH HOH . C 3 HOH U 97 2097 2097 HOH HOH . C 3 HOH U 98 2098 2098 HOH HOH . C 3 HOH U 99 2099 2099 HOH HOH . C 3 HOH U 100 2100 2100 HOH HOH . C 3 HOH U 101 2101 2101 HOH HOH . C 3 HOH U 102 2102 2102 HOH HOH . C 3 HOH U 103 2103 2103 HOH HOH . C 3 HOH U 104 2104 2104 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 N N1 SL1 . . . B 2 25.297 17.084 56.241 1 16.22 ? N1 SL1 1245 U 1 HETATM 2 C C1 SL1 . . . B 2 25.74 18.328 55.594 1 20.25 ? C1 SL1 1245 U 1 HETATM 3 C C2 SL1 . . . B 2 24.688 19.346 55.726 1 21 ? C2 SL1 1245 U 1 HETATM 4 O O1 SL1 . . . B 2 23.604 18.976 56.172 1 21.83 ? O1 SL1 1245 U 1 HETATM 5 N N2 SL1 . . . B 2 24.868 20.618 55.364 1 23.88 ? N2 SL1 1245 U 1 HETATM 6 C C3 SL1 . . . B 2 23.765 21.546 55.433 1 23.66 ? C3 SL1 1245 U 1 HETATM 7 C C4 SL1 . . . B 2 22.758 21.302 54.398 1 23.87 ? C4 SL1 1245 U 1 HETATM 8 O O3 SL1 . . . B 2 23.174 20.755 53.35 1 22.15 ? O3 SL1 1245 U 1 HETATM 9 N N3 SL1 . . . B 2 21.484 21.648 54.587 1 23.48 ? N3 SL1 1245 U 1 HETATM 10 C C5 SL1 . . . B 2 20.597 21.553 53.47 1 23.77 ? C5 SL1 1245 U 1 HETATM 11 C C6 SL1 . . . B 2 20.156 22.821 52.934 1 24.73 ? C6 SL1 1245 U 1 HETATM 12 O O2 SL1 . . . B 2 20.939 23.777 52.84 1 28.14 ? O2 SL1 1245 U 1 HETATM 13 C C7 SL1 . . . B 2 26.087 21.054 54.898 1 23.87 ? C7 SL1 1245 U 1 HETATM 14 C C9 SL1 . . . B 2 26.844 20.318 53.905 1 21.97 ? C9 SL1 1245 U 1 HETATM 15 C C8 SL1 . . . B 2 26.438 19.075 53.357 1 20.84 ? C8 SL1 1245 U 1 HETATM 16 N N4 SL1 . . . B 2 25.978 18.171 54.197 1 18.44 ? N4 SL1 1245 U 1 HETATM 17 C C10 SL1 . . . B 2 26.52 18.807 51.965 1 23.47 ? C10 SL1 1245 U 1 HETATM 18 C C11 SL1 . . . B 2 26.153 19.767 50.959 1 22.7 ? C11 SL1 1245 U 1 HETATM 19 C C12 SL1 . . . B 2 26.289 19.525 49.57 1 22.51 ? C12 SL1 1245 U 1 HETATM 20 C C13 SL1 . . . B 2 26.762 18.25 49.127 1 25.88 ? C13 SL1 1245 U 1 HETATM 21 C C14 SL1 . . . B 2 27.139 17.252 50.076 1 25.53 ? C14 SL1 1245 U 1 HETATM 22 C C15 SL1 . . . B 2 26.987 17.547 51.457 1 24.27 ? C15 SL1 1245 U 1 HETATM 23 C C16 SL1 . . . B 2 28.074 20.898 53.469 1 24.51 ? C16 SL1 1245 U 1 HETATM 24 C C17 SL1 . . . B 2 28.557 22.139 53.961 1 24.98 ? C17 SL1 1245 U 1 HETATM 25 C C18 SL1 . . . B 2 27.839 22.807 54.983 1 24.8 ? C18 SL1 1245 U 1 HETATM 26 C C19 SL1 . . . B 2 26.6 22.28 55.426 1 24.47 ? C19 SL1 1245 U 1 HETATM 27 C C20 SL1 . . . B 2 19.274 20.747 53.708 1 22.06 ? C20 SL1 1245 U 1 HETATM 28 C C21 SL1 . . . B 2 19.687 19.304 54.11 1 14.94 ? C21 SL1 1245 U 1 HETATM 29 C C22 SL1 . . . B 2 18.502 18.407 54.537 1 14.06 ? C22 SL1 1245 U 1 HETATM 30 N N5 SL1 . . . B 2 18.948 17.025 54.491 1 16.68 ? N5 SL1 1245 U 1 HETATM 31 C C23 SL1 . . . B 2 18.121 16.009 54.833 1 16.75 ? C23 SL1 1245 U 1 HETATM 32 N N6 SL1 . . . B 2 16.823 16.224 55.181 1 19.57 ? N6 SL1 1245 U 1 HETATM 33 N N7 SL1 . . . B 2 18.515 14.728 54.856 1 12.36 ? N7 SL1 1245 U 1 HETATM 34 S S SL1 . . . B 2 26.514 16.384 57.165 1 18.82 ? S SL1 1245 U 1 HETATM 35 O O4 SL1 . . . B 2 27.83 16.799 56.497 1 20.48 ? O4 SL1 1245 U 1 HETATM 36 O O5 SL1 . . . B 2 26.328 14.9 57.082 1 15.53 ? O5 SL1 1245 U 1 HETATM 37 C C24 SL1 . . . B 2 26.683 16.786 58.866 1 17.63 ? C24 SL1 1245 U 1 HETATM 38 C C25 SL1 . . . B 2 26.788 18.265 58.801 1 21.1 ? C25 SL1 1245 U 1 HETATM 39 C C26 SL1 . . . B 2 27.964 18.969 58.396 1 23.69 ? C26 SL1 1245 U 1 HETATM 40 C C27 SL1 . . . B 2 28.042 20.397 58.376 1 20.66 ? C27 SL1 1245 U 1 HETATM 41 C C28 SL1 . . . B 2 26.899 21.128 58.792 1 21.14 ? C28 SL1 1245 U 1 HETATM 42 C C29 SL1 . . . B 2 25.681 20.462 59.118 1 20.12 ? C29 SL1 1245 U 1 HETATM 43 C C30 SL1 . . . B 2 25.661 19.043 59.155 1 19.72 ? C30 SL1 1245 U 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #