data_5YLU
#
_model_server_result.job_id            mrHjEH36d45tY2bwCgFVYQ 
_model_server_result.datetime_utc      '2024-11-23 21:22:20' 
_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          5ylu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1101}' 
#
_entry.id    5YLU 
#
_exptl.entry_id    5YLU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              345.391 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine 
_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         120 
_cell.entry_id            5YLU 
_cell.length_a            104.82 
_cell.length_b            104.82 
_cell.length_c            367.08 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YLU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_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 
_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                      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
disulf ? disulf1 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
covale ? covale1 A NH1 ARG 214 A ARG 213 1_555 A ND2 ASN 251 A ASN 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.172 ? 
covale ? covale2 A C SER 385 A SER 384 1_555 A N BFD 386 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale3 A C BFD 386 A BFD 385 1_555 A N LYS 387 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B ND2 ASN 98 B ASN 99 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale5 B ND2 ASN 129 B ASN 130 1_555 I C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale6 B ND2 ASN 160 B ASN 161 1_555 J C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
metalc ? metalc1 A OD2 BFD 386 A BFD 385 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc2 A O THR 388 A THR 387 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc3 A OD1 ASP 727 A ASP 726 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
#
_chem_comp.formula           'C17 H16 F N3 O2 S' 
_chem_comp.formula_weight    345.391 
_chem_comp.id                HKT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Vonoprazan 
#
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
CBA NAJ HKT doub 262 n y 
CBA CAY HKT sing 263 n y 
NAJ CAT HKT sing 264 n y 
CAY CAU HKT doub 265 n y 
CAT CAN HKT doub 266 n y 
CAU CAN HKT sing 267 n y 
CAN SAA HKT sing 268 n n 
CAZ CAW HKT doub 269 n y 
CAZ CAX HKT sing 270 n y 
CAW CAR HKT sing 271 n y 
CAX CAS HKT doub 272 n y 
CAR FAB HKT sing 273 n n 
CAR CAM HKT doub 274 n y 
SAA OAD HKT doub 275 n n 
SAA OAC HKT doub 276 n n 
SAA NAI HKT sing 277 n n 
CAS CAM HKT sing 278 n y 
CAM CAL HKT sing 279 n n 
NAI CAL HKT sing 280 n y 
NAI CAO HKT sing 281 n y 
CAL CAQ HKT doub 282 n y 
CAO CAP HKT doub 283 n y 
CAQ CAP HKT sing 284 n y 
CAP CAV HKT sing 285 n n 
CAV NAK HKT sing 286 n n 
NAK CBB HKT sing 287 n n 
CAO H1 HKT sing 288 n n 
CAQ H2 HKT sing 289 n n 
CAS H3 HKT sing 290 n n 
CAT H4 HKT sing 291 n n 
CAU H5 HKT sing 292 n n 
CAV H6 HKT sing 293 n n 
CAV H7 HKT sing 294 n n 
CAW H8 HKT sing 295 n n 
CAX H9 HKT sing 296 n n 
CAY H10 HKT sing 297 n n 
CAZ H11 HKT sing 298 n n 
CBA H12 HKT sing 299 n n 
CBB H13 HKT sing 300 n n 
CBB H14 HKT sing 301 n n 
CBB H15 HKT sing 302 n n 
NAK H16 HKT sing 303 n n 
#
_atom_sites.entry_id                     5YLU 
_atom_sites.fract_transf_matrix[1][1]    0.00954 
_atom_sites.fract_transf_matrix[1][2]    0.005508 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011016 
_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]    0.002724 
_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 3 HKT A 1 1101 1101 HKT HKT . 
D 4 PCW A 1 1102 1102 PCW PCW . 
E 4 PCW A 1 1103 1103 PCW PCW . 
F 5 MG A 1 1104 1104 MG MG . 
G 6 CE1 A 1 1105 1105 CE1 CE1 . 
H 7 NAG B 1 301 301 NAG NAG . 
I 7 NAG B 1 302 302 NAG NAG . 
J 7 NAG B 1 303 303 NAG NAG . 
K 6 CE1 B 1 304 304 CE1 CE1 . 
L 8 HOH A 1 1201 1201 HOH HOH . 
L 8 HOH A 2 1202 1202 HOH HOH . 
L 8 HOH A 3 1203 1203 HOH HOH . 
L 8 HOH A 4 1204 1204 HOH HOH . 
L 8 HOH A 5 1205 1205 HOH HOH . 
L 8 HOH A 6 1206 1206 HOH HOH . 
L 8 HOH A 7 1207 1207 HOH HOH . 
L 8 HOH A 8 1208 1208 HOH HOH . 
L 8 HOH A 9 1209 1209 HOH HOH . 
L 8 HOH A 10 1210 1210 HOH HOH . 
L 8 HOH A 11 1211 1211 HOH HOH . 
L 8 HOH A 12 1212 1212 HOH HOH . 
L 8 HOH A 13 1213 1213 HOH HOH . 
L 8 HOH A 14 1214 1214 HOH HOH . 
L 8 HOH A 15 1215 1215 HOH HOH . 
L 8 HOH A 16 1216 1216 HOH HOH . 
L 8 HOH A 17 1217 1217 HOH HOH . 
L 8 HOH A 18 1218 1218 HOH HOH . 
L 8 HOH A 19 1219 1219 HOH HOH . 
L 8 HOH A 20 1220 1220 HOH HOH . 
L 8 HOH A 21 1221 1221 HOH HOH . 
L 8 HOH A 22 1222 1222 HOH HOH . 
L 8 HOH A 23 1223 1223 HOH HOH . 
L 8 HOH A 24 1224 1224 HOH HOH . 
L 8 HOH A 25 1225 1225 HOH HOH . 
L 8 HOH A 26 1226 1226 HOH HOH . 
L 8 HOH A 27 1227 1227 HOH HOH . 
L 8 HOH A 28 1228 1228 HOH HOH . 
L 8 HOH A 29 1229 1229 HOH HOH . 
L 8 HOH A 30 1230 1230 HOH HOH . 
M 8 HOH B 1 401 401 HOH HOH . 
M 8 HOH B 2 402 402 HOH HOH . 
M 8 HOH B 3 403 403 HOH HOH . 
M 8 HOH B 4 404 404 HOH HOH . 
M 8 HOH B 5 405 405 HOH HOH . 
M 8 HOH B 6 406 406 HOH HOH . 
M 8 HOH B 7 407 407 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 CAL HKT . . . C 3 49.366 -16.072 -2.775 1 45.56 ? CAL HKT 1101 A 1 
HETATM 2 C CAM HKT . . . C 3 49.215 -17.279 -3.642 1 44.49 ? CAM HKT 1101 A 1 
HETATM 3 C CAN HKT . . . C 3 48.44 -14.522 -5.471 1 48.55 ? CAN HKT 1101 A 1 
HETATM 4 C CAO HKT . . . C 3 49.076 -14.034 -1.882 1 49.81 ? CAO HKT 1101 A 1 
HETATM 5 C CAP HKT . . . C 3 49.983 -14.713 -1.067 1 48.39 ? CAP HKT 1101 A 1 
HETATM 6 C CAQ HKT . . . C 3 50.152 -15.979 -1.629 1 44.17 ? CAQ HKT 1101 A 1 
HETATM 7 C CAR HKT . . . C 3 50.279 -17.858 -4.319 1 48.52 ? CAR HKT 1101 A 1 
HETATM 8 C CAS HKT . . . C 3 47.95 -17.868 -3.701 1 40.63 ? CAS HKT 1101 A 1 
HETATM 9 C CAT HKT . . . C 3 48.314 -15.59 -6.374 1 50.69 ? CAT HKT 1101 A 1 
HETATM 10 C CAU HKT . . . C 3 49.26 -13.47 -5.879 1 44.85 ? CAU HKT 1101 A 1 
HETATM 11 C CAV HKT . . . C 3 50.67 -14.169 0.187 1 50.79 ? CAV HKT 1101 A 1 
HETATM 12 C CAW HKT . . . C 3 50.041 -19.006 -5.064 1 50.34 ? CAW HKT 1101 A 1 
HETATM 13 C CAX HKT . . . C 3 47.696 -19.003 -4.442 1 40.31 ? CAX HKT 1101 A 1 
HETATM 14 C CAY HKT . . . C 3 49.898 -13.509 -7.125 1 43 ? CAY HKT 1101 A 1 
HETATM 15 C CAZ HKT . . . C 3 48.762 -19.57 -5.124 1 51.4 ? CAZ HKT 1101 A 1 
HETATM 16 C CBA HKT . . . C 3 49.724 -14.6 -7.969 1 42.24 ? CBA HKT 1101 A 1 
HETATM 17 C CBB HKT . . . C 3 49.732 -15.715 1.74 1 41.89 ? CBB HKT 1101 A 1 
HETATM 18 F FAB HKT . . . C 3 51.529 -17.345 -4.284 1 51.1 ? FAB HKT 1101 A 1 
HETATM 19 N NAI HKT . . . C 3 48.75 -14.894 -2.857 1 51.5 ? NAI HKT 1101 A 1 
HETATM 20 N NAJ HKT . . . C 3 48.93 -15.609 -7.58 1 45.12 ? NAJ HKT 1101 A 1 
HETATM 21 N NAK HKT . . . C 3 49.83 -14.288 1.396 1 44.21 ? NAK HKT 1101 A 1 
HETATM 22 O OAC HKT . . . C 3 47.186 -13.205 -3.685 1 48.96 ? OAC HKT 1101 A 1 
HETATM 23 O OAD HKT . . . C 3 46.517 -15.338 -3.984 1 47.57 ? OAD HKT 1101 A 1 
HETATM 24 S SAA HKT . . . C 3 47.696 -14.505 -4.019 1 59.89 ? SAA HKT 1101 A 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           24 
#