data_6MCK
#
_model_server_result.job_id            aBZ0rOHt9387uikhupxF5Q 
_model_server_result.datetime_utc      '2025-07-01 21:11:35' 
_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          6mck 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":900}' 
#
_entry.id    6MCK 
#
_exptl.entry_id    6MCK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              413.472 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.67 
_cell.angle_gamma         90 
_cell.entry_id            6MCK 
_cell.length_a            127.41 
_cell.length_b            263.83 
_cell.length_c            164.13 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6MCK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
#
_chem_comp.formula           'C24 H23 N5 O2' 
_chem_comp.formula_weight    413.472 
_chem_comp.id                JDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     CB-5083 
#
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
O01 C02 JDP doub 173 n n 
N31 C02 JDP sing 174 n n 
C02 C03 JDP sing 175 n n 
C09 C08 JDP sing 176 n y 
C09 C10 JDP doub 177 n y 
C03 C08 JDP doub 178 n y 
C03 C04 JDP sing 179 n y 
C08 C07 JDP sing 180 n y 
C11 C10 JDP sing 181 n n 
C04 C05 JDP doub 182 n y 
C10 N12 JDP sing 183 n y 
C07 N12 JDP sing 184 n y 
C07 C06 JDP doub 185 n y 
N12 C13 JDP sing 186 n n 
C05 C06 JDP sing 187 n y 
C13 N30 JDP doub 188 n y 
C13 N14 JDP sing 189 n y 
N30 C29 JDP sing 190 n y 
N14 C15 JDP doub 191 n y 
C29 C28 JDP sing 192 n n 
C29 C24 JDP doub 193 n y 
C28 C27 JDP sing 194 n n 
C15 C24 JDP sing 195 n y 
C15 N16 JDP sing 196 n n 
C22 C21 JDP doub 197 n y 
C22 C23 JDP sing 198 n y 
C24 C25 JDP sing 199 n n 
C21 C20 JDP sing 200 n y 
C23 C18 JDP doub 201 n y 
N16 C17 JDP sing 202 n n 
C27 O26 JDP sing 203 n n 
C20 C19 JDP doub 204 n y 
C18 C19 JDP sing 205 n y 
C18 C17 JDP sing 206 n n 
C25 O26 JDP sing 207 n n 
C22 H1 JDP sing 208 n n 
C21 H2 JDP sing 209 n n 
C04 H3 JDP sing 210 n n 
C05 H4 JDP sing 211 n n 
C06 H5 JDP sing 212 n n 
C09 H6 JDP sing 213 n n 
C11 H7 JDP sing 214 n n 
C11 H8 JDP sing 215 n n 
C11 H9 JDP sing 216 n n 
N16 H10 JDP sing 217 n n 
C17 H11 JDP sing 218 n n 
C17 H12 JDP sing 219 n n 
C19 H13 JDP sing 220 n n 
C20 H14 JDP sing 221 n n 
C23 H15 JDP sing 222 n n 
C25 H16 JDP sing 223 n n 
C25 H17 JDP sing 224 n n 
C27 H18 JDP sing 225 n n 
C27 H19 JDP sing 226 n n 
C28 H20 JDP sing 227 n n 
C28 H21 JDP sing 228 n n 
N31 H22 JDP sing 229 n n 
N31 H23 JDP sing 230 n n 
#
_atom_sites.entry_id                     6MCK 
_atom_sites.fract_transf_matrix[1][1]    0.007849 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001909 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00379 
_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]    0.00627 
_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
M 2 JDP A 1 900 900 JDP CB5 . 
N 2 JDP B 1 900 900 JDP CB5 . 
O 2 JDP C 1 900 900 JDP CB5 . 
P 2 JDP D 1 900 900 JDP CB5 . 
Q 2 JDP E 1 900 900 JDP CB5 . 
R 2 JDP F 1 900 900 JDP CB5 . 
S 2 JDP G 1 900 900 JDP CB5 . 
T 2 JDP H 1 900 900 JDP CB5 . 
U 2 JDP I 1 900 900 JDP CB5 . 
V 2 JDP J 1 900 900 JDP CB5 . 
W 2 JDP K 1 900 900 JDP CB5 . 
X 2 JDP L 1 900 900 JDP CB5 . 
Y 3 HOH A 1 1001 26 HOH HOH . 
Y 3 HOH A 2 1002 13 HOH HOH . 
Y 3 HOH A 3 1003 1 HOH HOH . 
Z 3 HOH B 1 1001 14 HOH HOH . 
Z 3 HOH B 2 1002 2 HOH HOH . 
Z 3 HOH B 3 1003 27 HOH HOH . 
AA 3 HOH C 1 1001 28 HOH HOH . 
AA 3 HOH C 2 1002 15 HOH HOH . 
AA 3 HOH C 3 1003 3 HOH HOH . 
BA 3 HOH D 1 1001 4 HOH HOH . 
BA 3 HOH D 2 1002 29 HOH HOH . 
BA 3 HOH D 3 1003 16 HOH HOH . 
CA 3 HOH E 1 1001 5 HOH HOH . 
CA 3 HOH E 2 1002 17 HOH HOH . 
DA 3 HOH F 1 1001 18 HOH HOH . 
DA 3 HOH F 2 1002 6 HOH HOH . 
DA 3 HOH F 3 1003 31 HOH HOH . 
EA 3 HOH G 1 1001 7 HOH HOH . 
EA 3 HOH G 2 1002 19 HOH HOH . 
EA 3 HOH G 3 1003 25 HOH HOH . 
FA 3 HOH H 1 1001 8 HOH HOH . 
FA 3 HOH H 2 1002 20 HOH HOH . 
GA 3 HOH I 1 1001 21 HOH HOH . 
GA 3 HOH I 2 1002 9 HOH HOH . 
HA 3 HOH J 1 1001 32 HOH HOH . 
HA 3 HOH J 2 1002 22 HOH HOH . 
HA 3 HOH J 3 1003 10 HOH HOH . 
IA 3 HOH K 1 1001 33 HOH HOH . 
IA 3 HOH K 2 1002 23 HOH HOH . 
IA 3 HOH K 3 1003 11 HOH HOH . 
JA 3 HOH L 1 1001 24 HOH HOH . 
JA 3 HOH L 2 1002 12 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 C22 JDP . . . U 2 60.113 56.574 4.869 1 173.87 ? C22 JDP 900 I 1 
HETATM 2 C C21 JDP . . . U 2 60.356 55.216 5.023 1 166.88 ? C21 JDP 900 I 1 
HETATM 3 O O01 JDP . . . U 2 62.831 57.65 13.207 1 165.81 ? O01 JDP 900 I 1 
HETATM 4 C C02 JDP . . . U 2 61.816 57.698 12.519 1 161.09 ? C02 JDP 900 I 1 
HETATM 5 C C03 JDP . . . U 2 61.823 57.712 11.041 1 152.09 ? C03 JDP 900 I 1 
HETATM 6 C C04 JDP . . . U 2 61.043 56.84 10.316 1 149.1 ? C04 JDP 900 I 1 
HETATM 7 C C05 JDP . . . U 2 61.074 56.905 8.934 1 151.07 ? C05 JDP 900 I 1 
HETATM 8 C C06 JDP . . . U 2 61.858 57.82 8.25 1 144.84 ? C06 JDP 900 I 1 
HETATM 9 C C07 JDP . . . U 2 62.631 58.69 8.982 1 144.54 ? C07 JDP 900 I 1 
HETATM 10 C C08 JDP . . . U 2 62.613 58.643 10.376 1 147.51 ? C08 JDP 900 I 1 
HETATM 11 C C09 JDP . . . U 2 63.514 59.66 10.839 1 149.48 ? C09 JDP 900 I 1 
HETATM 12 C C10 JDP . . . U 2 64.029 60.273 9.77 1 148.95 ? C10 JDP 900 I 1 
HETATM 13 C C11 JDP . . . U 2 65.002 61.395 9.821 1 153.38 ? C11 JDP 900 I 1 
HETATM 14 N N12 JDP . . . U 2 63.526 59.684 8.596 1 144.78 ? N12 JDP 900 I 1 
HETATM 15 C C13 JDP . . . U 2 63.73 60.055 7.308 1 143.99 ? C13 JDP 900 I 1 
HETATM 16 N N14 JDP . . . U 2 63.869 59.114 6.409 1 146.55 ? N14 JDP 900 I 1 
HETATM 17 C C15 JDP . . . U 2 63.983 59.494 5.153 1 154.23 ? C15 JDP 900 I 1 
HETATM 18 N N16 JDP . . . U 2 64.19 58.451 4.342 1 162.37 ? N16 JDP 900 I 1 
HETATM 19 C C17 JDP . . . U 2 63.304 57.973 3.308 1 164.71 ? C17 JDP 900 I 1 
HETATM 20 C C18 JDP . . . U 2 62.304 57.008 3.908 1 168.79 ? C18 JDP 900 I 1 
HETATM 21 C C19 JDP . . . U 2 62.56 55.648 4.062 1 173.08 ? C19 JDP 900 I 1 
HETATM 22 C C20 JDP . . . U 2 61.598 54.766 4.609 1 173.78 ? C20 JDP 900 I 1 
HETATM 23 C C23 JDP . . . U 2 61.061 57.461 4.324 1 172.45 ? C23 JDP 900 I 1 
HETATM 24 C C24 JDP . . . U 2 63.959 60.868 4.764 1 151.64 ? C24 JDP 900 I 1 
HETATM 25 C C25 JDP . . . U 2 64.1 61.39 3.344 1 151.84 ? C25 JDP 900 I 1 
HETATM 26 O O26 JDP . . . U 2 64.655 62.726 3.261 1 148.01 ? O26 JDP 900 I 1 
HETATM 27 C C27 JDP . . . U 2 64.178 63.758 4.165 1 144.27 ? C27 JDP 900 I 1 
HETATM 28 C C28 JDP . . . U 2 63.731 63.259 5.556 1 145.2 ? C28 JDP 900 I 1 
HETATM 29 C C29 JDP . . . U 2 63.793 61.76 5.791 1 146.75 ? C29 JDP 900 I 1 
HETATM 30 N N30 JDP . . . U 2 63.651 61.347 7.054 1 142.27 ? N30 JDP 900 I 1 
HETATM 31 N N31 JDP . . . U 2 60.557 57.771 13.046 1 165.19 ? N31 JDP 900 I 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#