data_6PFA
#
_model_server_result.job_id            1SYNPHRu-1uqbJIzmJf4Xg 
_model_server_result.datetime_utc      '2024-11-28 06:28:04' 
_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          6pfa 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":603}' 
#
_entry.id    6PFA 
#
_exptl.entry_id    6PFA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              417.417 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-[({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)methyl]benzoic 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          95.72 
_cell.angle_gamma         90 
_cell.entry_id            6PFA 
_cell.length_a            213.21 
_cell.length_b            117.294 
_cell.length_c            222.817 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFA 
_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,N,O,EA,FA 1 1 
C,D,P,Q,R,S,T,U,V,W,X,Y,GA,HA 2 1 
E,Z,AA,BA,CA,DA,IA 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_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -213.21 0 0 
#
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 M N N 
? 4 R N N 
? 4 W N N 
? 4 BA N N 
#
_chem_comp.formula           'C22 H19 N5 O4' 
_chem_comp.formula_weight    417.417 
_chem_comp.id                OF4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2-[({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)methyl]benzoic 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
C20 C21 OF4 doub 376 n y 
C20 C19 OF4 sing 377 n y 
C21 C16 OF4 sing 378 n y 
O2 C14 OF4 doub 379 n n 
C19 C18 OF4 doub 380 n y 
C16 C15 OF4 sing 381 n n 
C16 C17 OF4 doub 382 n y 
C15 N5 OF4 sing 383 n n 
O4 C22 OF4 doub 384 n n 
N4 C4 OF4 sing 385 n n 
C18 C17 OF4 sing 386 n y 
C17 C22 OF4 sing 387 n n 
C22 O3 OF4 sing 388 n n 
C14 N5 OF4 sing 389 n n 
C14 C11 OF4 sing 390 n n 
C4 N2 OF4 sing 391 n n 
C4 N1 OF4 doub 392 n n 
N2 C3 OF4 sing 393 n n 
C11 C12 OF4 doub 394 n y 
C11 C10 OF4 sing 395 n y 
C12 C13 OF4 sing 396 n y 
N1 C1 OF4 sing 397 n n 
C3 O1 OF4 doub 398 n n 
C3 C2 OF4 sing 399 n n 
C10 C9 OF4 doub 400 n y 
C13 C8 OF4 doub 401 n y 
C1 C2 OF4 doub 402 n y 
C1 N3 OF4 sing 403 n y 
C2 C5 OF4 sing 404 n y 
C9 C8 OF4 sing 405 n y 
C8 C7 OF4 sing 406 n n 
N3 C6 OF4 sing 407 n y 
C5 C6 OF4 doub 408 n y 
C5 C7 OF4 sing 409 n n 
C10 H1 OF4 sing 410 n n 
C21 H2 OF4 sing 411 n n 
C12 H3 OF4 sing 412 n n 
C13 H4 OF4 sing 413 n n 
C15 H5 OF4 sing 414 n n 
C15 H6 OF4 sing 415 n n 
C18 H7 OF4 sing 416 n n 
C19 H8 OF4 sing 417 n n 
C20 H9 OF4 sing 418 n n 
C6 H10 OF4 sing 419 n n 
C7 H11 OF4 sing 420 n n 
C7 H12 OF4 sing 421 n n 
C9 H13 OF4 sing 422 n n 
N2 H14 OF4 sing 423 n n 
N3 H15 OF4 sing 424 n n 
N4 H16 OF4 sing 425 n n 
N4 H17 OF4 sing 426 n n 
N5 H18 OF4 sing 427 n n 
O3 H19 OF4 sing 428 n n 
#
_atom_sites.entry_id                     6PFA 
_atom_sites.fract_transf_matrix[1][1]    0.00469 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00047 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008526 
_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]    0.00451 
_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 OF4 A 1 603 603 OF4 M85 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 6 SO4 A 1 605 2 SO4 SO4 . 
K 2 NDP B 1 601 601 NDP NDP . 
L 3 UFP B 1 602 602 UFP UFP . 
M 4 OF4 B 1 603 603 OF4 M85 . 
N 5 MTX B 1 604 604 MTX MTX . 
O 6 SO4 B 1 605 1 SO4 SO4 . 
P 2 NDP C 1 601 601 NDP NDP . 
Q 3 UFP C 1 602 602 UFP UFP . 
R 4 OF4 C 1 603 603 OF4 M85 . 
S 5 MTX C 1 604 604 MTX MTX . 
T 6 SO4 C 1 605 3 SO4 SO4 . 
U 2 NDP D 1 601 601 NDP NDP . 
V 3 UFP D 1 602 602 UFP UFP . 
W 4 OF4 D 1 603 603 OF4 M85 . 
X 5 MTX D 1 604 604 MTX MTX . 
Y 6 SO4 D 1 605 4 SO4 SO4 . 
Z 2 NDP E 1 601 601 NDP NDP . 
AA 3 UFP E 1 602 602 UFP UFP . 
BA 4 OF4 E 1 603 603 OF4 M85 . 
CA 5 MTX E 1 604 604 MTX MTX . 
DA 6 SO4 E 1 605 5 SO4 SO4 . 
EA 7 HOH A 1 701 98 HOH HOH . 
EA 7 HOH A 2 702 59 HOH HOH . 
EA 7 HOH A 3 703 95 HOH HOH . 
EA 7 HOH A 4 704 63 HOH HOH . 
EA 7 HOH A 5 705 54 HOH HOH . 
EA 7 HOH A 6 706 4 HOH HOH . 
EA 7 HOH A 7 707 65 HOH HOH . 
EA 7 HOH A 8 708 100 HOH HOH . 
EA 7 HOH A 9 709 23 HOH HOH . 
EA 7 HOH A 10 710 6 HOH HOH . 
EA 7 HOH A 11 711 36 HOH HOH . 
EA 7 HOH A 12 712 45 HOH HOH . 
EA 7 HOH A 13 713 19 HOH HOH . 
EA 7 HOH A 14 714 72 HOH HOH . 
EA 7 HOH A 15 715 81 HOH HOH . 
EA 7 HOH A 16 716 62 HOH HOH . 
EA 7 HOH A 17 717 28 HOH HOH . 
EA 7 HOH A 18 718 70 HOH HOH . 
EA 7 HOH A 19 719 33 HOH HOH . 
EA 7 HOH A 20 720 110 HOH HOH . 
EA 7 HOH A 21 721 76 HOH HOH . 
EA 7 HOH A 22 722 96 HOH HOH . 
EA 7 HOH A 23 723 109 HOH HOH . 
EA 7 HOH A 24 724 69 HOH HOH . 
FA 7 HOH B 1 701 44 HOH HOH . 
FA 7 HOH B 2 702 1 HOH HOH . 
FA 7 HOH B 3 703 73 HOH HOH . 
FA 7 HOH B 4 704 3 HOH HOH . 
FA 7 HOH B 5 705 56 HOH HOH . 
FA 7 HOH B 6 706 67 HOH HOH . 
FA 7 HOH B 7 707 22 HOH HOH . 
FA 7 HOH B 8 708 13 HOH HOH . 
FA 7 HOH B 9 709 16 HOH HOH . 
FA 7 HOH B 10 710 55 HOH HOH . 
FA 7 HOH B 11 711 41 HOH HOH . 
FA 7 HOH B 12 712 99 HOH HOH . 
FA 7 HOH B 13 713 71 HOH HOH . 
FA 7 HOH B 14 714 27 HOH HOH . 
FA 7 HOH B 15 715 25 HOH HOH . 
FA 7 HOH B 16 716 2 HOH HOH . 
FA 7 HOH B 17 717 86 HOH HOH . 
FA 7 HOH B 18 718 50 HOH HOH . 
FA 7 HOH B 19 719 8 HOH HOH . 
FA 7 HOH B 20 720 12 HOH HOH . 
FA 7 HOH B 21 721 35 HOH HOH . 
FA 7 HOH B 22 722 11 HOH HOH . 
FA 7 HOH B 23 723 39 HOH HOH . 
FA 7 HOH B 24 724 32 HOH HOH . 
FA 7 HOH B 25 725 88 HOH HOH . 
FA 7 HOH B 26 726 40 HOH HOH . 
FA 7 HOH B 27 727 66 HOH HOH . 
FA 7 HOH B 28 728 101 HOH HOH . 
FA 7 HOH B 29 729 9 HOH HOH . 
FA 7 HOH B 30 730 43 HOH HOH . 
FA 7 HOH B 31 731 14 HOH HOH . 
FA 7 HOH B 32 732 105 HOH HOH . 
FA 7 HOH B 33 733 10 HOH HOH . 
FA 7 HOH B 34 734 18 HOH HOH . 
FA 7 HOH B 35 735 38 HOH HOH . 
FA 7 HOH B 36 736 57 HOH HOH . 
FA 7 HOH B 37 737 107 HOH HOH . 
GA 7 HOH C 1 701 15 HOH HOH . 
GA 7 HOH C 2 702 104 HOH HOH . 
GA 7 HOH C 3 703 48 HOH HOH . 
GA 7 HOH C 4 704 68 HOH HOH . 
GA 7 HOH C 5 705 29 HOH HOH . 
GA 7 HOH C 6 706 58 HOH HOH . 
GA 7 HOH C 7 707 30 HOH HOH . 
GA 7 HOH C 8 708 80 HOH HOH . 
GA 7 HOH C 9 709 78 HOH HOH . 
GA 7 HOH C 10 710 20 HOH HOH . 
GA 7 HOH C 11 711 90 HOH HOH . 
GA 7 HOH C 12 712 97 HOH HOH . 
GA 7 HOH C 13 713 24 HOH HOH . 
GA 7 HOH C 14 714 17 HOH HOH . 
GA 7 HOH C 15 715 64 HOH HOH . 
HA 7 HOH D 1 701 51 HOH HOH . 
HA 7 HOH D 2 702 77 HOH HOH . 
HA 7 HOH D 3 703 74 HOH HOH . 
HA 7 HOH D 4 704 42 HOH HOH . 
HA 7 HOH D 5 705 5 HOH HOH . 
HA 7 HOH D 6 706 83 HOH HOH . 
HA 7 HOH D 7 707 37 HOH HOH . 
HA 7 HOH D 8 708 92 HOH HOH . 
HA 7 HOH D 9 709 52 HOH HOH . 
HA 7 HOH D 10 710 61 HOH HOH . 
HA 7 HOH D 11 711 85 HOH HOH . 
HA 7 HOH D 12 712 94 HOH HOH . 
HA 7 HOH D 13 713 79 HOH HOH . 
HA 7 HOH D 14 714 26 HOH HOH . 
HA 7 HOH D 15 715 106 HOH HOH . 
HA 7 HOH D 16 716 102 HOH HOH . 
HA 7 HOH D 17 717 47 HOH HOH . 
HA 7 HOH D 18 718 82 HOH HOH . 
IA 7 HOH E 1 701 31 HOH HOH . 
IA 7 HOH E 2 702 7 HOH HOH . 
IA 7 HOH E 3 703 21 HOH HOH . 
IA 7 HOH E 4 704 84 HOH HOH . 
IA 7 HOH E 5 705 111 HOH HOH . 
IA 7 HOH E 6 706 46 HOH HOH . 
IA 7 HOH E 7 707 91 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 C10 OF4 . . . M 4 -57.036 -43.553 115.15 1 48.43 ? C10 OF4 603 B 1 
HETATM 2 C C11 OF4 . . . M 4 -57.275 -43.778 116.53 1 56.23 ? C11 OF4 603 B 1 
HETATM 3 C C21 OF4 . . . M 4 -57.536 -48.69 115.231 1 71.27 ? C21 OF4 603 B 1 
HETATM 4 C C22 OF4 . . . M 4 -61.338 -48.656 115.907 1 92.61 ? C22 OF4 603 B 1 
HETATM 5 C C1 OF4 . . . M 4 -53.748 -38.959 117.909 1 65.88 ? C1 OF4 603 B 1 
HETATM 6 C C12 OF4 . . . M 4 -57.142 -42.703 117.432 1 57.53 ? C12 OF4 603 B 1 
HETATM 7 C C13 OF4 . . . M 4 -56.79 -41.425 116.969 1 55.16 ? C13 OF4 603 B 1 
HETATM 8 C C14 OF4 . . . M 4 -57.662 -45.114 117.097 1 57.99 ? C14 OF4 603 B 1 
HETATM 9 C C15 OF4 . . . M 4 -58.823 -47.24 116.836 1 61.92 ? C15 OF4 603 B 1 
HETATM 10 C C16 OF4 . . . M 4 -58.788 -48.335 115.781 1 70.67 ? C16 OF4 603 B 1 
HETATM 11 C C17 OF4 . . . M 4 -59.975 -48.995 115.346 1 108.27 ? C17 OF4 603 B 1 
HETATM 12 C C18 OF4 . . . M 4 -59.859 -50.007 114.36 1 115.8 ? C18 OF4 603 B 1 
HETATM 13 C C19 OF4 . . . M 4 -58.605 -50.353 113.816 1 103.85 ? C19 OF4 603 B 1 
HETATM 14 C C2 OF4 . . . M 4 -54.126 -39.767 116.87 1 77.29 ? C2 OF4 603 B 1 
HETATM 15 C C20 OF4 . . . M 4 -57.443 -49.694 114.251 1 92.11 ? C20 OF4 603 B 1 
HETATM 16 C C3 OF4 . . . M 4 -53.261 -40.933 116.573 1 71.88 ? C3 OF4 603 B 1 
HETATM 17 C C4 OF4 . . . M 4 -51.898 -40.169 118.409 1 68.25 ? C4 OF4 603 B 1 
HETATM 18 C C5 OF4 . . . M 4 -55.337 -39.229 116.314 1 64.66 ? C5 OF4 603 B 1 
HETATM 19 C C6 OF4 . . . M 4 -55.646 -38.111 117.052 1 68.71 ? C6 OF4 603 B 1 
HETATM 20 C C7 OF4 . . . M 4 -56.145 -39.792 115.172 1 63.18 ? C7 OF4 603 B 1 
HETATM 21 C C8 OF4 . . . M 4 -56.544 -41.195 115.601 1 60.59 ? C8 OF4 603 B 1 
HETATM 22 C C9 OF4 . . . M 4 -56.671 -42.266 114.688 1 53.76 ? C9 OF4 603 B 1 
HETATM 23 N N1 OF4 . . . M 4 -52.627 -39.129 118.708 1 75.02 ? N1 OF4 603 B 1 
HETATM 24 N N2 OF4 . . . M 4 -52.183 -41.067 117.369 1 64.4 ? N2 OF4 603 B 1 
HETATM 25 N N3 OF4 . . . M 4 -54.671 -37.949 118.02 1 71.15 ? N3 OF4 603 B 1 
HETATM 26 N N4 OF4 . . . M 4 -50.745 -40.522 119.074 1 66.39 ? N4 OF4 603 B 1 
HETATM 27 N N5 OF4 . . . M 4 -58.406 -45.932 116.347 1 66.74 ? N5 OF4 603 B 1 
HETATM 28 O O1 OF4 . . . M 4 -53.5 -41.727 115.666 1 67.26 ? O1 OF4 603 B 1 
HETATM 29 O O2 OF4 . . . M 4 -57.313 -45.426 118.234 1 59.85 ? O2 OF4 603 B 1 
HETATM 30 O O3 OF4 . . . M 4 -61.576 -49.194 117.137 1 103.26 -1 O3 OF4 603 B 1 
HETATM 31 O O4 OF4 . . . M 4 -62.164 -47.952 115.328 1 72.66 ? O4 OF4 603 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           31 
#