data_6C1O
#
_model_server_result.job_id            -xiR5OPBORB0L2dD1BeadQ 
_model_server_result.datetime_utc      '2024-10-18 16:24:58' 
_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          6c1o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":801}' 
#
_entry.id    6C1O 
#
_exptl.entry_id    6C1O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              656.603 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-(3-{[3-(2,6-dichloro-3,5-dimethoxyphenyl)-7-{[4-(diethylamino)butyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]methyl}phenyl)prop-2-enamide 
_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          106.24 
_cell.angle_gamma         90 
_cell.entry_id            6C1O 
_cell.length_a            211.03 
_cell.length_b            50.384 
_cell.length_c            65.513 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6C1O 
_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,D,F 1 1 
B,E,G 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 E N N 
#
_chem_comp.formula           'C32 H39 Cl2 N7 O4' 
_chem_comp.formula_weight    656.603 
_chem_comp.id                MK9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-(3-{[3-(2,6-dichloro-3,5-dimethoxyphenyl)-7-{[4-(diethylamino)butyl]amino}-2-oxo-3,4-dihydropyrimido[4,5-d]pyrimidin-1(2H)-yl]methyl}phenyl)prop-2-enamide 
_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
CBR OAS MK9 sing 237 n n 
OAS CAP MK9 sing 238 n n 
CAP CAO MK9 doub 239 n y 
CAP CAQ MK9 sing 240 n y 
CLR CAQ MK9 sing 241 n n 
CAO CAN MK9 sing 242 n y 
CAQ CAL MK9 doub 243 n y 
CBI CBJ MK9 doub 244 n y 
CBI CBH MK9 sing 245 n y 
CBJ CBK MK9 sing 246 n y 
CAN OAT MK9 sing 247 n n 
CAN CAM MK9 doub 248 n y 
CBH CBG MK9 doub 249 n y 
CAL CAM MK9 sing 250 n y 
CAL NAI MK9 sing 251 n n 
CBS OAT MK9 sing 252 n n 
OAK CAH MK9 doub 253 n n 
CBK NBM MK9 sing 254 n n 
CBK CBL MK9 doub 255 n y 
NBM CBN MK9 sing 256 n n 
CAM CLU MK9 sing 257 n n 
NAI CAH MK9 sing 258 n n 
NAI CAJ MK9 sing 259 n n 
CAH NAG MK9 sing 260 n n 
CBG CBL MK9 sing 261 n y 
CBG CAW MK9 sing 262 n n 
CBN CBO MK9 sing 263 n n 
CBN OBQ MK9 doub 264 n n 
CBO CBP MK9 doub 265 n n 
CAJ C5 MK9 sing 266 n n 
CAW NAG MK9 sing 267 n n 
NAG C4 MK9 sing 268 n n 
C5 C4 MK9 doub 269 n y 
C5 C6 MK9 sing 270 n y 
C4 N3 MK9 sing 271 n y 
C6 N1 MK9 doub 272 n y 
N3 C2 MK9 doub 273 n y 
N1 C2 MK9 sing 274 n y 
C2 NAV MK9 sing 275 n n 
CAX NAV MK9 sing 276 n n 
CAO H1 MK9 sing 277 n n 
CBS H2 MK9 sing 278 n n 
CBS H3 MK9 sing 279 n n 
CBS H4 MK9 sing 280 n n 
CBR H5 MK9 sing 281 n n 
CBR H6 MK9 sing 282 n n 
CBR H7 MK9 sing 283 n n 
CAJ H8 MK9 sing 284 n n 
CAJ H9 MK9 sing 285 n n 
C6 H10 MK9 sing 286 n n 
NAV H11 MK9 sing 287 n n 
CAX H12 MK9 sing 288 n n 
CAX H13 MK9 sing 289 n n 
CAW H15 MK9 sing 290 n n 
CAW H16 MK9 sing 291 n n 
CBL H17 MK9 sing 292 n n 
CBH H18 MK9 sing 293 n n 
CBI H19 MK9 sing 294 n n 
CBJ H20 MK9 sing 295 n n 
NBM H21 MK9 sing 296 n n 
CBO H22 MK9 sing 297 n n 
CBP H24 MK9 sing 298 n n 
CBP H25 MK9 sing 299 n n 
CAX CAY MK9 sing 300 n n 
CAY CAZ MK9 sing 301 n n 
CAZ C7 MK9 sing 302 n n 
C7 N2 MK9 sing 303 n n 
N2 C9 MK9 sing 304 n n 
N2 C8 MK9 sing 305 n n 
C8 C10 MK9 sing 306 n n 
C9 C11 MK9 sing 307 n n 
CAY H14 MK9 sing 308 n n 
CAY H23 MK9 sing 309 n n 
CAZ H26 MK9 sing 310 n n 
CAZ H27 MK9 sing 311 n n 
C7 H28 MK9 sing 312 n n 
C7 H29 MK9 sing 313 n n 
C9 H30 MK9 sing 314 n n 
C9 H31 MK9 sing 315 n n 
C8 H32 MK9 sing 316 n n 
C8 H33 MK9 sing 317 n n 
C10 H34 MK9 sing 318 n n 
C10 H35 MK9 sing 319 n n 
C10 H36 MK9 sing 320 n n 
C11 H37 MK9 sing 321 n n 
C11 H38 MK9 sing 322 n n 
C11 H39 MK9 sing 323 n n 
#
_atom_sites.entry_id                     6C1O 
_atom_sites.fract_transf_matrix[1][1]    0.004739 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00138 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019848 
_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]    0.015899 
_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 MK9 A 1 801 1 MK9 MK9 . 
D 3 SO4 A 1 802 1 SO4 SO4 . 
E 2 MK9 B 1 801 2 MK9 MK9 . 
F 4 HOH A 1 901 2 HOH HOH . 
F 4 HOH A 2 902 13 HOH HOH . 
F 4 HOH A 3 903 9 HOH HOH . 
F 4 HOH A 4 904 8 HOH HOH . 
F 4 HOH A 5 905 10 HOH HOH . 
F 4 HOH A 6 906 3 HOH HOH . 
F 4 HOH A 7 907 6 HOH HOH . 
G 4 HOH B 1 901 1 HOH HOH . 
G 4 HOH B 2 902 7 HOH HOH . 
G 4 HOH B 3 903 11 HOH HOH . 
G 4 HOH B 4 904 14 HOH HOH . 
G 4 HOH B 5 905 12 HOH HOH . 
G 4 HOH B 6 906 4 HOH HOH . 
G 4 HOH B 7 907 5 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 CL CLR MK9 . . . C 2 -12.782 -15.242 12.941 1 56.87 ? CLR MK9 801 A 1 
HETATM 2 C CAQ MK9 . . . C 2 -12.682 -14.452 11.397 1 55.53 ? CAQ MK9 801 A 1 
HETATM 3 C CAO MK9 . . . C 2 -11.384 -13.944 9.418 1 56.12 ? CAO MK9 801 A 1 
HETATM 4 C CAN MK9 . . . C 2 -12.44 -13.193 8.921 1 56.64 ? CAN MK9 801 A 1 
HETATM 5 O OAT MK9 . . . C 2 -12.392 -12.559 7.711 1 57.22 ? OAT MK9 801 A 1 
HETATM 6 C CBS MK9 . . . C 2 -11.338 -11.628 7.481 1 57.68 ? CBS MK9 801 A 1 
HETATM 7 C CAM MK9 . . . C 2 -13.616 -13.079 9.666 1 56.59 ? CAM MK9 801 A 1 
HETATM 8 CL CLU MK9 . . . C 2 -14.928 -12.143 9.034 1 61.99 ? CLU MK9 801 A 1 
HETATM 9 C CAP MK9 . . . C 2 -11.484 -14.572 10.654 1 55.51 ? CAP MK9 801 A 1 
HETATM 10 O OAS MK9 . . . C 2 -10.485 -15.331 11.204 1 54.03 ? OAS MK9 801 A 1 
HETATM 11 C CBR MK9 . . . C 2 -9.161 -15.234 10.683 1 53.33 ? CBR MK9 801 A 1 
HETATM 12 C CAL MK9 . . . C 2 -13.748 -13.706 10.896 1 54.57 ? CAL MK9 801 A 1 
HETATM 13 N NAI MK9 . . . C 2 -14.984 -13.531 11.623 1 51.55 ? NAI MK9 801 A 1 
HETATM 14 C CAJ MK9 . . . C 2 -14.831 -12.609 12.75 1 50.25 ? CAJ MK9 801 A 1 
HETATM 15 C C5 MK9 . . . C 2 -16.154 -12.34 13.383 1 49.25 ? C5 MK9 801 A 1 
HETATM 16 C C6 MK9 . . . C 2 -16.488 -11.06 13.972 1 48.43 ? C6 MK9 801 A 1 
HETATM 17 N N1 MK9 . . . C 2 -17.681 -10.867 14.519 1 48.23 ? N1 MK9 801 A 1 
HETATM 18 C C2 MK9 . . . C 2 -18.558 -11.898 14.492 1 50.02 ? C2 MK9 801 A 1 
HETATM 19 N NAV MK9 . . . C 2 -19.756 -11.662 15.051 1 52.38 ? NAV MK9 801 A 1 
HETATM 20 C CAX MK9 . . . C 2 -20.847 -12.616 15.14 1 56.48 ? CAX MK9 801 A 1 
HETATM 21 N N3 MK9 . . . C 2 -18.323 -13.126 13.955 1 49.03 ? N3 MK9 801 A 1 
HETATM 22 C C4 MK9 . . . C 2 -17.125 -13.346 13.377 1 50.04 ? C4 MK9 801 A 1 
HETATM 23 C CAH MK9 . . . C 2 -15.854 -14.631 11.792 1 51.85 ? CAH MK9 801 A 1 
HETATM 24 O OAK MK9 . . . C 2 -15.795 -15.592 11.045 1 51.84 ? OAK MK9 801 A 1 
HETATM 25 N NAG MK9 . . . C 2 -16.825 -14.602 12.835 1 53.1 ? NAG MK9 801 A 1 
HETATM 26 C CAW MK9 . . . C 2 -17.932 -15.604 12.744 1 57.19 ? CAW MK9 801 A 1 
HETATM 27 C CBG MK9 . . . C 2 -19.129 -15.211 11.896 1 60.45 ? CBG MK9 801 A 1 
HETATM 28 C CBL MK9 . . . C 2 -20.407 -15.252 12.441 1 62.83 ? CBL MK9 801 A 1 
HETATM 29 C CBH MK9 . . . C 2 -18.988 -14.848 10.564 1 61.19 ? CBH MK9 801 A 1 
HETATM 30 C CBI MK9 . . . C 2 -20.092 -14.512 9.802 1 62.07 ? CBI MK9 801 A 1 
HETATM 31 C CBJ MK9 . . . C 2 -21.361 -14.547 10.353 1 62.94 ? CBJ MK9 801 A 1 
HETATM 32 C CBK MK9 . . . C 2 -21.524 -14.912 11.684 1 64.86 ? CBK MK9 801 A 1 
HETATM 33 N NBM MK9 . . . C 2 -22.803 -14.969 12.295 1 67.02 ? NBM MK9 801 A 1 
HETATM 34 C CBN MK9 . . . C 2 -23.83 -14.097 12.19 1 69.58 ? CBN MK9 801 A 1 
HETATM 35 O OBQ MK9 . . . C 2 -23.769 -13.073 11.499 1 69.53 ? OBQ MK9 801 A 1 
HETATM 36 C CBO MK9 . . . C 2 -25.042 -14.461 12.969 1 70.29 ? CBO MK9 801 A 1 
HETATM 37 C CBP MK9 . . . C 2 -26.138 -13.735 12.952 1 70.34 ? CBP MK9 801 A 1 
HETATM 38 C CAY MK9 . . . C 2 -21.964 -12.107 16.036 1 59.55 ? CAY MK9 801 A 1 
HETATM 39 C CAZ MK9 . . . C 2 -23.283 -12.824 15.848 1 62.61 ? CAZ MK9 801 A 1 
HETATM 40 C C7 MK9 . . . C 2 -24.164 -12.799 17.076 1 65.74 ? C7 MK9 801 A 1 
HETATM 41 N N2 MK9 . . . C 2 -25.6 -12.845 16.827 1 68.05 ? N2 MK9 801 A 1 
HETATM 42 C C9 MK9 . . . C 2 -26.353 -13.512 17.992 1 69.32 ? C9 MK9 801 A 1 
HETATM 43 C C8 MK9 . . . C 2 -26.158 -11.443 16.528 1 69.08 ? C8 MK9 801 A 1 
HETATM 44 C C10 MK9 . . . C 2 -27.434 -11.463 15.715 1 69.74 ? C10 MK9 801 A 1 
HETATM 45 C C11 MK9 . . . C 2 -26.306 -15.025 17.946 1 69.52 ? C11 MK9 801 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           45 
#