data_6PFB
#
_model_server_result.job_id            1kd0-XjmswtV-9l4TBBPEQ 
_model_server_result.datetime_utc      '2024-11-25 08:30:47' 
_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          6pfb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":603}' 
#
_entry.id    6PFB 
#
_exptl.entry_id    6PFB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              431.444 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)phenyl]propanoic acid' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.75 
_cell.angle_gamma         90 
_cell.entry_id            6PFB 
_cell.length_a            213.994 
_cell.length_b            116.238 
_cell.length_c            221.672 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFB 
_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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,H,I,J,K,L,M 1 1 
C,D,N,O,P,Q,R,S,T,U 2 1 
E,V,W,X,Y 3 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_658 -x+1,y,-z+3 -1 0 0 0 1 0 0 0 -1 158.925217 0 662.732004 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 H N N 
? 4 L N N 
? 4 P N N 
? 4 T N N 
? 4 X N N 
#
_chem_comp.formula           'C23 H21 N5 O4' 
_chem_comp.formula_weight    431.444 
_chem_comp.id                OG4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)phenyl]propanoic acid' 
_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
N4 C4 OG4 sing 374 n n 
N1 C4 OG4 doub 375 n n 
N1 C1 OG4 sing 376 n n 
C4 N2 OG4 sing 377 n n 
N3 C1 OG4 sing 378 n y 
N3 C6 OG4 sing 379 n y 
C1 C2 OG4 doub 380 n y 
O2 C14 OG4 doub 381 n n 
N2 C3 OG4 sing 382 n n 
C12 C13 OG4 doub 383 n y 
C12 C11 OG4 sing 384 n y 
C6 C5 OG4 doub 385 n y 
C13 C8 OG4 sing 386 n y 
C2 C3 OG4 sing 387 n n 
C2 C5 OG4 sing 388 n y 
C22 C21 OG4 sing 389 n n 
C22 C23 OG4 sing 390 n n 
O3 C23 OG4 doub 391 n n 
C3 O1 OG4 doub 392 n n 
C14 C11 OG4 sing 393 n n 
C14 N5 OG4 sing 394 n n 
C5 C7 OG4 sing 395 n n 
C21 C16 OG4 sing 396 n n 
C11 C10 OG4 doub 397 n y 
C23 O4 OG4 sing 398 n n 
C16 C17 OG4 doub 399 n y 
C16 C15 OG4 sing 400 n y 
C17 C18 OG4 sing 401 n y 
C8 C7 OG4 sing 402 n n 
C8 C9 OG4 doub 403 n y 
N5 C15 OG4 sing 404 n n 
C15 C20 OG4 doub 405 n y 
C18 C19 OG4 doub 406 n y 
C10 C9 OG4 sing 407 n y 
C20 C19 OG4 sing 408 n y 
C10 H1 OG4 sing 409 n n 
C12 H2 OG4 sing 410 n n 
C13 H3 OG4 sing 411 n n 
C17 H4 OG4 sing 412 n n 
C18 H5 OG4 sing 413 n n 
C19 H6 OG4 sing 414 n n 
C20 H7 OG4 sing 415 n n 
C21 H8 OG4 sing 416 n n 
C21 H9 OG4 sing 417 n n 
C22 H10 OG4 sing 418 n n 
C22 H11 OG4 sing 419 n n 
C6 H12 OG4 sing 420 n n 
C7 H13 OG4 sing 421 n n 
C7 H14 OG4 sing 422 n n 
C9 H15 OG4 sing 423 n n 
N2 H16 OG4 sing 424 n n 
N3 H17 OG4 sing 425 n n 
N4 H18 OG4 sing 426 n n 
N4 H19 OG4 sing 427 n n 
N5 H20 OG4 sing 428 n n 
O4 H21 OG4 sing 429 n n 
#
_atom_sites.entry_id                     6PFB 
_atom_sites.fract_transf_matrix[1][1]    0.004673 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000389 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008603 
_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]    0.004527 
_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
F 2 NDP A 1 601 601 NDP NDP . 
G 3 UFP A 1 602 602 UFP UFP . 
H 4 OG4 A 1 603 603 OG4 TS7 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 2 NDP B 1 601 601 NDP NDP . 
K 3 UFP B 1 602 602 UFP UFP . 
L 4 OG4 B 1 603 603 OG4 TS7 . 
M 5 MTX B 1 604 604 MTX MTX . 
N 2 NDP C 1 601 601 NDP NDP . 
O 3 UFP C 1 602 602 UFP UFP . 
P 4 OG4 C 1 603 603 OG4 TS7 . 
Q 5 MTX C 1 604 604 MTX MTX . 
R 2 NDP D 1 601 601 NDP NDP . 
S 3 UFP D 1 602 602 UFP UFP . 
T 4 OG4 D 1 603 603 OG4 TS7 . 
U 5 MTX D 1 604 604 MTX MTX . 
V 2 NDP E 1 601 601 NDP NDP . 
W 3 UFP E 1 602 602 UFP UFP . 
X 4 OG4 E 1 603 603 OG4 TS7 . 
Y 5 MTX E 1 604 604 MTX MTX . 
#
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 C1 OG4 . . . L 4 10.969 117.895 242.305 1 115.44 ? C1 OG4 603 B 1 
HETATM 2 C C10 OG4 . . . L 4 4.707 116.618 242.226 1 105.72 ? C10 OG4 603 B 1 
HETATM 3 C C11 OG4 . . . L 4 4.748 117.504 243.296 1 104.48 ? C11 OG4 603 B 1 
HETATM 4 C C12 OG4 . . . L 4 5.795 118.411 243.408 1 99.78 ? C12 OG4 603 B 1 
HETATM 5 C C13 OG4 . . . L 4 6.798 118.435 242.446 1 95.65 ? C13 OG4 603 B 1 
HETATM 6 C C14 OG4 . . . L 4 3.667 117.473 244.336 1 99.45 ? C14 OG4 603 B 1 
HETATM 7 C C15 OG4 . . . L 4 1.531 116.234 244.815 1 108.04 ? C15 OG4 603 B 1 
HETATM 8 C C16 OG4 . . . L 4 0.511 117.156 245.07 1 123.06 ? C16 OG4 603 B 1 
HETATM 9 C C17 OG4 . . . L 4 -0.599 116.759 245.809 1 132.1 ? C17 OG4 603 B 1 
HETATM 10 C C18 OG4 . . . L 4 -0.703 115.462 246.294 1 132.14 ? C18 OG4 603 B 1 
HETATM 11 C C19 OG4 . . . L 4 0.309 114.547 246.04 1 112.7 ? C19 OG4 603 B 1 
HETATM 12 C C2 OG4 . . . L 4 9.798 117.209 242.001 1 109.2 ? C2 OG4 603 B 1 
HETATM 13 C C20 OG4 . . . L 4 1.418 114.935 245.3 1 104.36 ? C20 OG4 603 B 1 
HETATM 14 C C21 OG4 . . . L 4 0.578 118.57 244.563 1 122.24 ? C21 OG4 603 B 1 
HETATM 15 C C22 OG4 . . . L 4 -0.624 119.342 245.026 1 122.67 ? C22 OG4 603 B 1 
HETATM 16 C C23 OG4 . . . L 4 -1.433 119.806 243.851 1 131.13 ? C23 OG4 603 B 1 
HETATM 17 C C3 OG4 . . . L 4 9.5 115.982 242.737 1 119.39 ? C3 OG4 603 B 1 
HETATM 18 C C4 OG4 . . . L 4 11.633 116.446 243.894 1 107 ? C4 OG4 603 B 1 
HETATM 19 C C5 OG4 . . . L 4 9.146 117.93 240.985 1 98 ? C5 OG4 603 B 1 
HETATM 20 C C6 OG4 . . . L 4 9.937 119.038 240.692 1 109.55 ? C6 OG4 603 B 1 
HETATM 21 C C7 OG4 . . . L 4 7.841 117.571 240.336 1 105.58 ? C7 OG4 603 B 1 
HETATM 22 C C8 OG4 . . . L 4 6.756 117.551 241.373 1 100.82 ? C8 OG4 603 B 1 
HETATM 23 C C9 OG4 . . . L 4 5.711 116.641 241.265 1 110.41 ? C9 OG4 603 B 1 
HETATM 24 N N1 OG4 . . . L 4 11.891 117.532 243.24 1 124.81 ? N1 OG4 603 B 1 
HETATM 25 N N2 OG4 . . . L 4 10.488 115.716 243.645 1 103.28 ? N2 OG4 603 B 1 
HETATM 26 N N3 OG4 . . . L 4 11.046 119.001 241.508 1 109.46 ? N3 OG4 603 B 1 
HETATM 27 N N4 OG4 . . . L 4 12.537 115.941 244.924 1 105.99 ? N4 OG4 603 B 1 
HETATM 28 N N5 OG4 . . . L 4 2.728 116.568 244.043 1 108.43 ? N5 OG4 603 B 1 
HETATM 29 O O1 OG4 . . . L 4 8.531 115.232 242.626 1 122.19 ? O1 OG4 603 B 1 
HETATM 30 O O2 OG4 . . . L 4 3.632 118.18 245.34 1 95.62 ? O2 OG4 603 B 1 
HETATM 31 O O3 OG4 . . . L 4 -0.602 120.166 242.84 1 128.88 -1 O3 OG4 603 B 1 
HETATM 32 O O4 OG4 . . . L 4 -2.656 119.871 243.769 1 133.17 ? O4 OG4 603 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#