data_6VKO
#
_model_server_result.job_id            DxzE-9NlSBMG6nBFouPc0g 
_model_server_result.datetime_utc      '2025-01-10 13:37:54' 
_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          6vko 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1101}' 
#
_entry.id    6VKO 
#
_exptl.entry_id    6VKO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              485.495 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          111.36 
_cell.angle_gamma         90 
_cell.entry_id            6VKO 
_cell.length_a            139.701 
_cell.length_b            129.751 
_cell.length_c            102.72 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VKO 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,U 1 1 
B,I,J,K,L,V 2 1 
C,M,N,O,P,W 3 1 
D,Q,R,S,T,X 4 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 E N N 
? 2 I N N 
? 2 M N N 
? 2 Q 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
disulf ? disulf1 A SG CYS 206 A CYS 845 1_555 A SG CYS 206 A CYS 845 2_657 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
disulf ? disulf2 B SG CYS 206 B CYS 845 1_555 D SG CYS 206 D CYS 845 2_658 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
disulf ? disulf3 C SG CYS 206 C CYS 845 1_555 C SG CYS 206 C CYS 845 2_658 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
#
_chem_comp.formula           'C25 H23 N7 O4' 
_chem_comp.formula_weight    485.495 
_chem_comp.id                L1S 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate' 
_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
C17 C16 L1S doub 173 n y 
C17 C18 L1S sing 174 n y 
C16 C14 L1S sing 175 n y 
C18 C19 L1S doub 176 n y 
O3 C15 L1S doub 177 n n 
C14 C15 L1S sing 178 n n 
C14 C13 L1S doub 179 n y 
C15 N4 L1S sing 180 n n 
C19 C13 L1S sing 181 n y 
C19 N5 L1S sing 182 n y 
C13 N3 L1S sing 183 n y 
N5 C12 L1S doub 184 n y 
N3 C12 L1S sing 185 n y 
C12 C11 L1S sing 186 n n 
C11 C20 L1S doub 187 n y 
C11 C10 L1S sing 188 n y 
C20 C21 L1S sing 189 n y 
C10 C9 L1S doub 190 n y 
C3 N L1S doub 191 n y 
C3 C2 L1S sing 192 n y 
O1 C1 L1S doub 193 n n 
N C4 L1S sing 194 n y 
C21 C8 L1S doub 195 n y 
C5 C6 L1S sing 196 n n 
C5 N1 L1S sing 197 n n 
C9 C8 L1S sing 198 n y 
C6 N2 L1S sing 199 n n 
C8 C7 L1S sing 200 n n 
C1 C2 L1S sing 201 n n 
C1 O L1S sing 202 n n 
C2 C24 L1S doub 203 n y 
C4 N1 L1S sing 204 n n 
C4 N6 L1S doub 205 n y 
N1 C23 L1S sing 206 n n 
C7 N2 L1S sing 207 n n 
C7 O2 L1S doub 208 n n 
N2 C22 L1S sing 209 n n 
O C L1S sing 210 n n 
C24 N6 L1S sing 211 n y 
C23 C22 L1S sing 212 n n 
C5 H1 L1S sing 213 n n 
C5 H2 L1S sing 214 n n 
C6 H3 L1S sing 215 n n 
C6 H4 L1S sing 216 n n 
C9 H5 L1S sing 217 n n 
C10 H6 L1S sing 218 n n 
N3 H7 L1S sing 219 n n 
N4 H8 L1S sing 220 n n 
N4 H9 L1S sing 221 n n 
C16 H10 L1S sing 222 n n 
C17 H11 L1S sing 223 n n 
C18 H12 L1S sing 224 n n 
C20 H14 L1S sing 225 n n 
C21 H15 L1S sing 226 n n 
C22 H16 L1S sing 227 n n 
C22 H17 L1S sing 228 n n 
C23 H18 L1S sing 229 n n 
C23 H19 L1S sing 230 n n 
C3 H20 L1S sing 231 n n 
C24 H21 L1S sing 232 n n 
C H22 L1S sing 233 n n 
C H23 L1S sing 234 n n 
C H24 L1S sing 235 n n 
#
_atom_sites.entry_id                     6VKO 
_atom_sites.fract_transf_matrix[1][1]    0.007158 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002799 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007707 
_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]    0.010453 
_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
E 2 L1S A 1 1101 1101 L1S XXX . 
F 3 SO4 A 1 1102 4 SO4 SO4 . 
G 3 SO4 A 1 1103 5 SO4 SO4 . 
H 3 SO4 A 1 1104 9 SO4 SO4 . 
I 2 L1S B 1 1101 1101 L1S XXX . 
J 3 SO4 B 1 1102 3 SO4 SO4 . 
K 3 SO4 B 1 1103 8 SO4 SO4 . 
L 3 SO4 B 1 1104 12 SO4 SO4 . 
M 2 L1S C 1 1101 1101 L1S XXX . 
N 3 SO4 C 1 1102 1 SO4 SO4 . 
O 3 SO4 C 1 1103 6 SO4 SO4 . 
P 3 SO4 C 1 1104 10 SO4 SO4 . 
Q 2 L1S D 1 1101 1101 L1S XXX . 
R 3 SO4 D 1 1102 2 SO4 SO4 . 
S 3 SO4 D 1 1103 7 SO4 SO4 . 
T 3 SO4 D 1 1104 11 SO4 SO4 . 
U 4 HOH A 1 1201 31 HOH HOH . 
U 4 HOH A 2 1202 26 HOH HOH . 
U 4 HOH A 3 1203 30 HOH HOH . 
U 4 HOH A 4 1204 22 HOH HOH . 
U 4 HOH A 5 1205 27 HOH HOH . 
U 4 HOH A 6 1206 4 HOH HOH . 
V 4 HOH B 1 1201 6 HOH HOH . 
V 4 HOH B 2 1202 9 HOH HOH . 
V 4 HOH B 3 1203 5 HOH HOH . 
V 4 HOH B 4 1204 10 HOH HOH . 
V 4 HOH B 5 1205 25 HOH HOH . 
V 4 HOH B 6 1206 8 HOH HOH . 
V 4 HOH B 7 1207 7 HOH HOH . 
V 4 HOH B 8 1208 21 HOH HOH . 
W 4 HOH C 1 1201 11 HOH HOH . 
W 4 HOH C 2 1202 12 HOH HOH . 
W 4 HOH C 3 1203 29 HOH HOH . 
W 4 HOH C 4 1204 24 HOH HOH . 
W 4 HOH C 5 1205 13 HOH HOH . 
W 4 HOH C 6 1206 15 HOH HOH . 
W 4 HOH C 7 1207 14 HOH HOH . 
X 4 HOH D 1 1201 16 HOH HOH . 
X 4 HOH D 2 1202 18 HOH HOH . 
X 4 HOH D 3 1203 1 HOH HOH . 
X 4 HOH D 4 1204 19 HOH HOH . 
X 4 HOH D 5 1205 23 HOH HOH . 
X 4 HOH D 6 1206 28 HOH HOH . 
X 4 HOH D 7 1207 2 HOH HOH . 
X 4 HOH D 8 1208 20 HOH HOH . 
X 4 HOH D 9 1209 3 HOH HOH . 
X 4 HOH D 10 1210 17 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 O O3 L1S . . . E 2 29.39 -24.326 71.776 1 61.1 ? O3 L1S 1101 A 1 
HETATM 2 C C4 L1S . . . E 2 39.732 -30.021 62.553 1 126.81 ? C4 L1S 1101 A 1 
HETATM 3 C C5 L1S . . . E 2 37.709 -29.271 63.751 1 109.24 ? C5 L1S 1101 A 1 
HETATM 4 C C6 L1S . . . E 2 38.062 -28.319 64.882 1 104.8 ? C6 L1S 1101 A 1 
HETATM 5 N N1 L1S . . . E 2 38.799 -30.225 63.519 1 114.16 ? N1 L1S 1101 A 1 
HETATM 6 C C7 L1S . . . E 2 37.763 -28.994 67.279 1 90.04 ? C7 L1S 1101 A 1 
HETATM 7 C C8 L1S . . . E 2 36.736 -27.927 67.471 1 80.59 ? C8 L1S 1101 A 1 
HETATM 8 N N2 L1S . . . E 2 38.394 -29.078 66.093 1 100.48 ? N2 L1S 1101 A 1 
HETATM 9 C C9 L1S . . . E 2 37.091 -26.582 67.541 1 74.32 ? C9 L1S 1101 A 1 
HETATM 10 C C10 L1S . . . E 2 36.144 -25.616 67.829 1 67.6 ? C10 L1S 1101 A 1 
HETATM 11 C C11 L1S . . . E 2 34.816 -25.967 68.051 1 65.88 ? C11 L1S 1101 A 1 
HETATM 12 C C12 L1S . . . E 2 33.822 -24.964 68.472 1 58.7 ? C12 L1S 1101 A 1 
HETATM 13 N N3 L1S . . . E 2 32.862 -25.206 69.355 1 57.28 ? N3 L1S 1101 A 1 
HETATM 14 C C13 L1S . . . E 2 32.164 -24.011 69.46 1 57.83 ? C13 L1S 1101 A 1 
HETATM 15 C C14 L1S . . . E 2 31.057 -23.635 70.239 1 57.67 ? C14 L1S 1101 A 1 
HETATM 16 C C15 L1S . . . E 2 30.326 -24.667 71.049 1 57.83 ? C15 L1S 1101 A 1 
HETATM 17 N N4 L1S . . . E 2 30.695 -25.942 70.924 1 53.89 ? N4 L1S 1101 A 1 
HETATM 18 C C16 L1S . . . E 2 30.584 -22.321 70.172 1 55.39 ? C16 L1S 1101 A 1 
HETATM 19 C C17 L1S . . . E 2 31.17 -21.397 69.316 1 53.97 ? C17 L1S 1101 A 1 
HETATM 20 C C18 L1S . . . E 2 32.246 -21.753 68.519 1 50.04 ? C18 L1S 1101 A 1 
HETATM 21 C C19 L1S . . . E 2 32.73 -23.052 68.616 1 52.55 ? C19 L1S 1101 A 1 
HETATM 22 N N5 L1S . . . E 2 33.792 -23.688 68 1 54.43 ? N5 L1S 1101 A 1 
HETATM 23 C C20 L1S . . . E 2 34.458 -27.308 67.951 1 70.88 ? C20 L1S 1101 A 1 
HETATM 24 C C21 L1S . . . E 2 35.403 -28.273 67.661 1 77.26 ? C21 L1S 1101 A 1 
HETATM 25 O O2 L1S . . . E 2 38.032 -29.739 68.206 1 92.09 ? O2 L1S 1101 A 1 
HETATM 26 C C22 L1S . . . E 2 39.489 -30.022 65.854 1 106.14 ? C22 L1S 1101 A 1 
HETATM 27 C C23 L1S . . . E 2 39.113 -30.97 64.741 1 108.77 ? C23 L1S 1101 A 1 
HETATM 28 N N L1S . . . E 2 39.338 -29.347 61.459 1 130.6 ? N L1S 1101 A 1 
HETATM 29 C C3 L1S . . . E 2 40.275 -29.16 60.522 1 132.98 ? C3 L1S 1101 A 1 
HETATM 30 N N6 L1S . . . E 2 40.967 -30.501 62.788 1 130.34 ? N6 L1S 1101 A 1 
HETATM 31 C C24 L1S . . . E 2 41.87 -30.277 61.826 1 136.59 ? C24 L1S 1101 A 1 
HETATM 32 C C2 L1S . . . E 2 41.583 -29.606 60.643 1 140.41 ? C2 L1S 1101 A 1 
HETATM 33 C C1 L1S . . . E 2 42.6 -29.286 59.603 1 145.53 ? C1 L1S 1101 A 1 
HETATM 34 O O1 L1S . . . E 2 42.344 -28.77 58.542 1 136.59 ? O1 L1S 1101 A 1 
HETATM 35 O O L1S . . . E 2 43.837 -29.626 59.976 1 156.27 ? O L1S 1101 A 1 
HETATM 36 C C L1S . . . E 2 44.223 -31.005 59.77 1 155.36 ? C L1S 1101 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           36 
#