data_5I9I
#
_model_server_result.job_id            VfRhebSRvvh5OD7MlbmZWg 
_model_server_result.datetime_utc      '2025-01-10 16:14:56' 
_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          5i9i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5I9I 
#
_exptl.entry_id    5I9I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              666.771 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "N-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[ 4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide" 
_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          115.5 
_cell.angle_gamma         90 
_cell.entry_id            5I9I 
_cell.length_a            115.9 
_cell.length_b            82.41 
_cell.length_c            96.47 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5I9I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,G 1 1 
B,D,E,F,H 2 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 
#
_chem_comp.formula           'C36 H38 F4 N4 O2 S' 
_chem_comp.formula_weight    666.771 
_chem_comp.id                5HV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "N-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[ 4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Darapladib 
#
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
O68 C67 5HV doub 1 n n 
C63 C60 5HV sing 2 n n 
C63 C66 5HV sing 3 n n 
C60 C57 5HV sing 4 n n 
C67 C66 5HV sing 5 n n 
C67 N69 5HV sing 6 n n 
C66 C56 5HV doub 7 n n 
C57 C56 5HV sing 8 n n 
C56 N55 5HV sing 9 n n 
N69 C70 5HV doub 10 n n 
N55 C70 5HV sing 11 n n 
N55 C52 5HV sing 12 n n 
C70 S71 5HV sing 13 n n 
C12 C09 5HV sing 14 n n 
O51 C50 5HV doub 15 n n 
C72 S71 5HV sing 16 n n 
C72 C75 5HV sing 17 n n 
C52 C50 5HV sing 18 n n 
C50 N22 5HV sing 19 n n 
C09 N08 5HV sing 20 n n 
C75 C84 5HV doub 21 n y 
C75 C76 5HV sing 22 n y 
C84 C82 5HV sing 23 n y 
C16 N08 5HV sing 24 n n 
C16 C19 5HV sing 25 n n 
N22 C19 5HV sing 26 n n 
N22 C23 5HV sing 27 n n 
N08 C05 5HV sing 28 n n 
C76 C78 5HV doub 29 n y 
C82 C80 5HV doub 30 n y 
C05 C01 5HV sing 31 n n 
C23 C26 5HV sing 32 n n 
C78 C80 5HV sing 33 n y 
C80 F81 5HV sing 34 n n 
C34 C26 5HV doub 35 n y 
C34 C32 5HV sing 36 n y 
C26 C27 5HV sing 37 n y 
C32 C31 5HV doub 38 n y 
C27 C29 5HV doub 39 n y 
C31 C29 5HV sing 40 n y 
C31 C36 5HV sing 41 n n 
C44 C36 5HV doub 42 n y 
C44 C42 5HV sing 43 n y 
C36 C37 5HV sing 44 n y 
C42 C41 5HV doub 45 n y 
C37 C39 5HV doub 46 n y 
C41 C39 5HV sing 47 n y 
C41 C46 5HV sing 48 n n 
F48 C46 5HV sing 49 n n 
C46 F47 5HV sing 50 n n 
C46 F49 5HV sing 51 n n 
C01 H1 5HV sing 52 n n 
C01 H2 5HV sing 53 n n 
C01 H3 5HV sing 54 n n 
C05 H4 5HV sing 55 n n 
C05 H5 5HV sing 56 n n 
C09 H7 5HV sing 57 n n 
C09 H8 5HV sing 58 n n 
C12 H9 5HV sing 59 n n 
C12 H10 5HV sing 60 n n 
C12 H11 5HV sing 61 n n 
C16 H12 5HV sing 62 n n 
C16 H13 5HV sing 63 n n 
C19 H14 5HV sing 64 n n 
C19 H15 5HV sing 65 n n 
C23 H16 5HV sing 66 n n 
C23 H17 5HV sing 67 n n 
C27 H18 5HV sing 68 n n 
C29 H19 5HV sing 69 n n 
C32 H20 5HV sing 70 n n 
C34 H21 5HV sing 71 n n 
C37 H22 5HV sing 72 n n 
C39 H23 5HV sing 73 n n 
C42 H24 5HV sing 74 n n 
C44 H25 5HV sing 75 n n 
C52 H26 5HV sing 76 n n 
C52 H27 5HV sing 77 n n 
C57 H28 5HV sing 78 n n 
C57 H29 5HV sing 79 n n 
C60 H30 5HV sing 80 n n 
C60 H31 5HV sing 81 n n 
C63 H32 5HV sing 82 n n 
C63 H33 5HV sing 83 n n 
C72 H34 5HV sing 84 n n 
C72 H35 5HV sing 85 n n 
C76 H36 5HV sing 86 n n 
C78 H37 5HV sing 87 n n 
C82 H38 5HV sing 88 n n 
C84 H39 5HV sing 89 n n 
#
_atom_sites.entry_id                     5I9I 
_atom_sites.fract_transf_matrix[1][1]    0.008628 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004115 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012134 
_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]    0.011484 
_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 5HV A 1 501 1 5HV LIG . 
D 2 5HV B 1 501 1 5HV LIG . 
E 3 SO4 B 1 502 1 SO4 SO4 . 
F 3 SO4 B 1 503 2 SO4 SO4 . 
G 4 HOH A 1 601 1 HOH HOH . 
G 4 HOH A 2 602 5 HOH HOH . 
G 4 HOH A 3 603 3 HOH HOH . 
G 4 HOH A 4 604 6 HOH HOH . 
H 4 HOH B 1 601 4 HOH HOH . 
H 4 HOH B 2 602 2 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 C01 5HV . . . C 2 205.297 20.02 116.328 1 37.19 ? C01 5HV 501 A 1 
HETATM 2 C C05 5HV . . . C 2 204.268 20.415 117.375 1 40.57 ? C05 5HV 501 A 1 
HETATM 3 N N08 5HV . . . C 2 203.026 20.927 116.82 1 34.67 ? N08 5HV 501 A 1 
HETATM 4 C C09 5HV . . . C 2 201.912 20.037 117.011 1 41.6 ? C09 5HV 501 A 1 
HETATM 5 C C12 5HV . . . C 2 202.123 18.642 116.366 1 34.98 ? C12 5HV 501 A 1 
HETATM 6 C C16 5HV . . . C 2 203.128 21.373 115.423 1 32.52 ? C16 5HV 501 A 1 
HETATM 7 C C19 5HV . . . C 2 203.409 22.911 115.419 1 35.07 ? C19 5HV 501 A 1 
HETATM 8 N N22 5HV . . . C 2 203.202 23.55 114.075 1 39.87 ? N22 5HV 501 A 1 
HETATM 9 C C23 5HV . . . C 2 204.304 24.253 113.347 1 31.75 ? C23 5HV 501 A 1 
HETATM 10 C C26 5HV . . . C 2 204.905 25.393 114.235 1 33.96 ? C26 5HV 501 A 1 
HETATM 11 C C27 5HV . . . C 2 206.237 25.788 114.065 1 33.63 ? C27 5HV 501 A 1 
HETATM 12 C C29 5HV . . . C 2 206.765 26.804 114.862 1 32.67 ? C29 5HV 501 A 1 
HETATM 13 C C31 5HV . . . C 2 205.928 27.434 115.811 1 41.66 ? C31 5HV 501 A 1 
HETATM 14 C C32 5HV . . . C 2 204.617 27.037 115.986 1 38.79 ? C32 5HV 501 A 1 
HETATM 15 C C34 5HV . . . C 2 204.093 26.011 115.182 1 32.2 ? C34 5HV 501 A 1 
HETATM 16 C C36 5HV . . . C 2 206.416 28.415 116.675 1 39.47 ? C36 5HV 501 A 1 
HETATM 17 C C37 5HV . . . C 2 207.719 28.192 117.183 1 46.35 ? C37 5HV 501 A 1 
HETATM 18 C C39 5HV . . . C 2 208.288 29.088 118.094 1 43.01 ? C39 5HV 501 A 1 
HETATM 19 C C41 5HV . . . C 2 207.544 30.199 118.524 1 39.93 ? C41 5HV 501 A 1 
HETATM 20 C C42 5HV . . . C 2 206.221 30.419 118.046 1 40.78 ? C42 5HV 501 A 1 
HETATM 21 C C44 5HV . . . C 2 205.65 29.52 117.122 1 37.9 ? C44 5HV 501 A 1 
HETATM 22 C C46 5HV . . . C 2 208.246 31.125 119.538 1 39.02 ? C46 5HV 501 A 1 
HETATM 23 F F47 5HV . . . C 2 208.874 32.136 118.899 1 38.06 ? F47 5HV 501 A 1 
HETATM 24 F F48 5HV . . . C 2 207.355 31.602 120.425 1 42.82 ? F48 5HV 501 A 1 
HETATM 25 F F49 5HV . . . C 2 209.102 30.34 120.216 1 28.27 ? F49 5HV 501 A 1 
HETATM 26 C C50 5HV . . . C 2 201.875 23.494 113.456 1 33.42 ? C50 5HV 501 A 1 
HETATM 27 O O51 5HV . . . C 2 200.937 22.933 113.995 1 29.71 ? O51 5HV 501 A 1 
HETATM 28 C C52 5HV . . . C 2 201.642 24.139 112.107 1 33.71 ? C52 5HV 501 A 1 
HETATM 29 N N55 5HV . . . C 2 200.201 24.438 112.016 1 32.16 ? N55 5HV 501 A 1 
HETATM 30 C C56 5HV . . . C 2 199.366 23.489 111.524 1 31.51 ? C56 5HV 501 A 1 
HETATM 31 C C57 5HV . . . C 2 199.666 22.062 111.005 1 23.84 ? C57 5HV 501 A 1 
HETATM 32 C C60 5HV . . . C 2 198.352 21.528 110.539 1 29.05 ? C60 5HV 501 A 1 
HETATM 33 C C63 5HV . . . C 2 197.292 22.525 110.855 1 28.19 ? C63 5HV 501 A 1 
HETATM 34 C C66 5HV . . . C 2 197.989 23.751 111.433 1 30.41 ? C66 5HV 501 A 1 
HETATM 35 C C67 5HV . . . C 2 197.515 25.002 111.872 1 29.03 ? C67 5HV 501 A 1 
HETATM 36 O O68 5HV . . . C 2 196.324 25.252 111.786 1 27.13 ? O68 5HV 501 A 1 
HETATM 37 N N69 5HV . . . C 2 198.398 25.931 112.369 1 33.38 ? N69 5HV 501 A 1 
HETATM 38 C C70 5HV . . . C 2 199.72 25.645 112.444 1 30.63 ? C70 5HV 501 A 1 
HETATM 39 S S71 5HV . . . C 2 200.849 26.859 113.082 1 30.65 ? S71 5HV 501 A 1 
HETATM 40 C C72 5HV . . . C 2 199.915 28.403 113.378 1 42.4 ? C72 5HV 501 A 1 
HETATM 41 C C75 5HV . . . C 2 200.589 29.141 114.564 1 35.92 ? C75 5HV 501 A 1 
HETATM 42 C C76 5HV . . . C 2 200.431 28.617 115.862 1 28.69 ? C76 5HV 501 A 1 
HETATM 43 C C78 5HV . . . C 2 201.033 29.263 116.935 1 36.61 ? C78 5HV 501 A 1 
HETATM 44 C C80 5HV . . . C 2 201.788 30.424 116.727 1 40 ? C80 5HV 501 A 1 
HETATM 45 F F81 5HV . . . C 2 202.353 31.028 117.768 1 46.58 ? F81 5HV 501 A 1 
HETATM 46 C C82 5HV . . . C 2 201.94 30.943 115.43 1 35.64 ? C82 5HV 501 A 1 
HETATM 47 C C84 5HV . . . C 2 201.337 30.293 114.339 1 32.24 ? C84 5HV 501 A 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           47 
#