data_6YNR
#
_model_server_result.job_id            YKgb_BlslBMc5mgSRq0ITQ 
_model_server_result.datetime_utc      '2024-10-13 02:27:20' 
_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          6ynr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":403}' 
#
_entry.id    6YNR 
#
_exptl.entry_id    6YNR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              145.161 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,7-naphthyridin-8-amine 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            6YNR 
_cell.length_a            72.406 
_cell.length_b            74.264 
_cell.length_c            80.225 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YNR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 A C SEP 13 A SEP 10 1_555 A N GLU 14 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_chem_comp.formula           'C8 H7 N3' 
_chem_comp.formula_weight    145.161 
_chem_comp.id                O72 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,7-naphthyridin-8-amine 
_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
C5 C4 O72 doub 267 n y 
C5 C6 O72 sing 268 n y 
C4 C3 O72 sing 269 n y 
C6 N2 O72 doub 270 n y 
N2 C7 O72 sing 271 n y 
C3 C7 O72 doub 272 n y 
C3 C2 O72 sing 273 n y 
C7 C O72 sing 274 n y 
C2 C1 O72 doub 275 n y 
C N O72 sing 276 n n 
C N1 O72 doub 277 n y 
C1 N1 O72 sing 278 n y 
C1 H1 O72 sing 279 n n 
C2 H2 O72 sing 280 n n 
C6 H3 O72 sing 281 n n 
C5 H4 O72 sing 282 n n 
C4 H5 O72 sing 283 n n 
N H6 O72 sing 284 n n 
N H7 O72 sing 285 n n 
#
_atom_sites.entry_id                     6YNR 
_atom_sites.fract_transf_matrix[1][1]    0.013811 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013465 
_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]    0.012465 
_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 3 MPD A 1 401 1 MPD MPD . 
D 4 DMS A 1 402 2 DMS DMS . 
E 5 O72 A 1 403 1 O72 L52 . 
F 6 HOH A 1 501 217 HOH HOH . 
F 6 HOH A 2 502 8 HOH HOH . 
F 6 HOH A 3 503 175 HOH HOH . 
F 6 HOH A 4 504 58 HOH HOH . 
F 6 HOH A 5 505 206 HOH HOH . 
F 6 HOH A 6 506 165 HOH HOH . 
F 6 HOH A 7 507 164 HOH HOH . 
F 6 HOH A 8 508 75 HOH HOH . 
F 6 HOH A 9 509 130 HOH HOH . 
F 6 HOH A 10 510 149 HOH HOH . 
F 6 HOH A 11 511 35 HOH HOH . 
F 6 HOH A 12 512 1 HOH HOH . 
F 6 HOH A 13 513 56 HOH HOH . 
F 6 HOH A 14 514 95 HOH HOH . 
F 6 HOH A 15 515 24 HOH HOH . 
F 6 HOH A 16 516 199 HOH HOH . 
F 6 HOH A 17 517 3 HOH HOH . 
F 6 HOH A 18 518 107 HOH HOH . 
F 6 HOH A 19 519 2 HOH HOH . 
F 6 HOH A 20 520 190 HOH HOH . 
F 6 HOH A 21 521 39 HOH HOH . 
F 6 HOH A 22 522 100 HOH HOH . 
F 6 HOH A 23 523 108 HOH HOH . 
F 6 HOH A 24 524 32 HOH HOH . 
F 6 HOH A 25 525 205 HOH HOH . 
F 6 HOH A 26 526 198 HOH HOH . 
F 6 HOH A 27 527 214 HOH HOH . 
F 6 HOH A 28 528 218 HOH HOH . 
F 6 HOH A 29 529 80 HOH HOH . 
F 6 HOH A 30 530 181 HOH HOH . 
F 6 HOH A 31 531 226 HOH HOH . 
F 6 HOH A 32 532 192 HOH HOH . 
F 6 HOH A 33 533 132 HOH HOH . 
F 6 HOH A 34 534 114 HOH HOH . 
F 6 HOH A 35 535 44 HOH HOH . 
F 6 HOH A 36 536 197 HOH HOH . 
F 6 HOH A 37 537 166 HOH HOH . 
F 6 HOH A 38 538 55 HOH HOH . 
F 6 HOH A 39 539 228 HOH HOH . 
F 6 HOH A 40 540 89 HOH HOH . 
F 6 HOH A 41 541 9 HOH HOH . 
F 6 HOH A 42 542 22 HOH HOH . 
F 6 HOH A 43 543 17 HOH HOH . 
F 6 HOH A 44 544 158 HOH HOH . 
F 6 HOH A 45 545 40 HOH HOH . 
F 6 HOH A 46 546 42 HOH HOH . 
F 6 HOH A 47 547 79 HOH HOH . 
F 6 HOH A 48 548 170 HOH HOH . 
F 6 HOH A 49 549 5 HOH HOH . 
F 6 HOH A 50 550 213 HOH HOH . 
F 6 HOH A 51 551 46 HOH HOH . 
F 6 HOH A 52 552 182 HOH HOH . 
F 6 HOH A 53 553 43 HOH HOH . 
F 6 HOH A 54 554 71 HOH HOH . 
F 6 HOH A 55 555 151 HOH HOH . 
F 6 HOH A 56 556 180 HOH HOH . 
F 6 HOH A 57 557 186 HOH HOH . 
F 6 HOH A 58 558 59 HOH HOH . 
F 6 HOH A 59 559 4 HOH HOH . 
F 6 HOH A 60 560 64 HOH HOH . 
F 6 HOH A 61 561 222 HOH HOH . 
F 6 HOH A 62 562 65 HOH HOH . 
F 6 HOH A 63 563 148 HOH HOH . 
F 6 HOH A 64 564 122 HOH HOH . 
F 6 HOH A 65 565 101 HOH HOH . 
F 6 HOH A 66 566 173 HOH HOH . 
F 6 HOH A 67 567 96 HOH HOH . 
F 6 HOH A 68 568 194 HOH HOH . 
F 6 HOH A 69 569 26 HOH HOH . 
F 6 HOH A 70 570 53 HOH HOH . 
F 6 HOH A 71 571 81 HOH HOH . 
F 6 HOH A 72 572 167 HOH HOH . 
F 6 HOH A 73 573 153 HOH HOH . 
F 6 HOH A 74 574 52 HOH HOH . 
F 6 HOH A 75 575 88 HOH HOH . 
F 6 HOH A 76 576 115 HOH HOH . 
F 6 HOH A 77 577 45 HOH HOH . 
F 6 HOH A 78 578 11 HOH HOH . 
F 6 HOH A 79 579 187 HOH HOH . 
F 6 HOH A 80 580 72 HOH HOH . 
F 6 HOH A 81 581 135 HOH HOH . 
F 6 HOH A 82 582 121 HOH HOH . 
F 6 HOH A 83 583 172 HOH HOH . 
F 6 HOH A 84 584 171 HOH HOH . 
F 6 HOH A 85 585 74 HOH HOH . 
F 6 HOH A 86 586 76 HOH HOH . 
F 6 HOH A 87 587 93 HOH HOH . 
F 6 HOH A 88 588 169 HOH HOH . 
F 6 HOH A 89 589 90 HOH HOH . 
F 6 HOH A 90 590 133 HOH HOH . 
F 6 HOH A 91 591 14 HOH HOH . 
F 6 HOH A 92 592 223 HOH HOH . 
F 6 HOH A 93 593 109 HOH HOH . 
F 6 HOH A 94 594 177 HOH HOH . 
F 6 HOH A 95 595 37 HOH HOH . 
F 6 HOH A 96 596 128 HOH HOH . 
F 6 HOH A 97 597 120 HOH HOH . 
F 6 HOH A 98 598 125 HOH HOH . 
F 6 HOH A 99 599 200 HOH HOH . 
F 6 HOH A 100 600 119 HOH HOH . 
F 6 HOH A 101 601 112 HOH HOH . 
F 6 HOH A 102 602 99 HOH HOH . 
F 6 HOH A 103 603 184 HOH HOH . 
F 6 HOH A 104 604 6 HOH HOH . 
F 6 HOH A 105 605 33 HOH HOH . 
F 6 HOH A 106 606 63 HOH HOH . 
F 6 HOH A 107 607 134 HOH HOH . 
F 6 HOH A 108 608 102 HOH HOH . 
F 6 HOH A 109 609 196 HOH HOH . 
F 6 HOH A 110 610 23 HOH HOH . 
F 6 HOH A 111 611 16 HOH HOH . 
F 6 HOH A 112 612 123 HOH HOH . 
F 6 HOH A 113 613 138 HOH HOH . 
F 6 HOH A 114 614 139 HOH HOH . 
F 6 HOH A 115 615 113 HOH HOH . 
F 6 HOH A 116 616 129 HOH HOH . 
F 6 HOH A 117 617 48 HOH HOH . 
F 6 HOH A 118 618 230 HOH HOH . 
F 6 HOH A 119 619 28 HOH HOH . 
F 6 HOH A 120 620 124 HOH HOH . 
F 6 HOH A 121 621 189 HOH HOH . 
F 6 HOH A 122 622 193 HOH HOH . 
F 6 HOH A 123 623 57 HOH HOH . 
F 6 HOH A 124 624 224 HOH HOH . 
F 6 HOH A 125 625 61 HOH HOH . 
F 6 HOH A 126 626 66 HOH HOH . 
F 6 HOH A 127 627 209 HOH HOH . 
F 6 HOH A 128 628 41 HOH HOH . 
F 6 HOH A 129 629 219 HOH HOH . 
F 6 HOH A 130 630 67 HOH HOH . 
F 6 HOH A 131 631 78 HOH HOH . 
F 6 HOH A 132 632 191 HOH HOH . 
F 6 HOH A 133 633 161 HOH HOH . 
F 6 HOH A 134 634 229 HOH HOH . 
F 6 HOH A 135 635 118 HOH HOH . 
F 6 HOH A 136 636 105 HOH HOH . 
F 6 HOH A 137 637 87 HOH HOH . 
F 6 HOH A 138 638 12 HOH HOH . 
F 6 HOH A 139 639 50 HOH HOH . 
F 6 HOH A 140 640 150 HOH HOH . 
F 6 HOH A 141 641 7 HOH HOH . 
F 6 HOH A 142 642 18 HOH HOH . 
F 6 HOH A 143 643 15 HOH HOH . 
F 6 HOH A 144 644 62 HOH HOH . 
F 6 HOH A 145 645 21 HOH HOH . 
F 6 HOH A 146 646 147 HOH HOH . 
F 6 HOH A 147 647 131 HOH HOH . 
F 6 HOH A 148 648 210 HOH HOH . 
F 6 HOH A 149 649 126 HOH HOH . 
F 6 HOH A 150 650 13 HOH HOH . 
F 6 HOH A 151 651 69 HOH HOH . 
F 6 HOH A 152 652 103 HOH HOH . 
F 6 HOH A 153 653 179 HOH HOH . 
F 6 HOH A 154 654 137 HOH HOH . 
F 6 HOH A 155 655 185 HOH HOH . 
F 6 HOH A 156 656 84 HOH HOH . 
F 6 HOH A 157 657 77 HOH HOH . 
F 6 HOH A 158 658 70 HOH HOH . 
F 6 HOH A 159 659 36 HOH HOH . 
F 6 HOH A 160 660 106 HOH HOH . 
F 6 HOH A 161 661 159 HOH HOH . 
F 6 HOH A 162 662 60 HOH HOH . 
F 6 HOH A 163 663 168 HOH HOH . 
F 6 HOH A 164 664 216 HOH HOH . 
F 6 HOH A 165 665 10 HOH HOH . 
F 6 HOH A 166 666 29 HOH HOH . 
F 6 HOH A 167 667 51 HOH HOH . 
F 6 HOH A 168 668 227 HOH HOH . 
F 6 HOH A 169 669 127 HOH HOH . 
F 6 HOH A 170 670 38 HOH HOH . 
F 6 HOH A 171 671 27 HOH HOH . 
F 6 HOH A 172 672 34 HOH HOH . 
F 6 HOH A 173 673 19 HOH HOH . 
F 6 HOH A 174 674 195 HOH HOH . 
F 6 HOH A 175 675 215 HOH HOH . 
F 6 HOH A 176 676 163 HOH HOH . 
F 6 HOH A 177 677 221 HOH HOH . 
F 6 HOH A 178 678 225 HOH HOH . 
F 6 HOH A 179 679 47 HOH HOH . 
F 6 HOH A 180 680 117 HOH HOH . 
F 6 HOH A 181 681 94 HOH HOH . 
F 6 HOH A 182 682 110 HOH HOH . 
F 6 HOH A 183 683 220 HOH HOH . 
F 6 HOH A 184 684 204 HOH HOH . 
F 6 HOH A 185 685 174 HOH HOH . 
F 6 HOH A 186 686 178 HOH HOH . 
F 6 HOH A 187 687 176 HOH HOH . 
F 6 HOH A 188 688 201 HOH HOH . 
F 6 HOH A 189 689 146 HOH HOH . 
F 6 HOH A 190 690 97 HOH HOH . 
F 6 HOH A 191 691 207 HOH HOH . 
F 6 HOH A 192 692 154 HOH HOH . 
F 6 HOH A 193 693 212 HOH HOH . 
F 6 HOH A 194 694 152 HOH HOH . 
F 6 HOH A 195 695 85 HOH HOH . 
F 6 HOH A 196 696 83 HOH HOH . 
F 6 HOH A 197 697 203 HOH HOH . 
F 6 HOH A 198 698 208 HOH HOH . 
F 6 HOH A 199 699 82 HOH HOH . 
F 6 HOH A 200 700 86 HOH HOH . 
F 6 HOH A 201 701 202 HOH HOH . 
G 6 HOH B 1 101 54 HOH HOH . 
G 6 HOH B 2 102 25 HOH HOH . 
G 6 HOH B 3 103 143 HOH HOH . 
G 6 HOH B 4 104 116 HOH HOH . 
G 6 HOH B 5 105 144 HOH HOH . 
G 6 HOH B 6 106 145 HOH HOH . 
G 6 HOH B 7 107 141 HOH HOH . 
G 6 HOH B 8 108 91 HOH HOH . 
G 6 HOH B 9 109 140 HOH HOH . 
G 6 HOH B 10 110 104 HOH HOH . 
G 6 HOH B 11 111 92 HOH HOH . 
G 6 HOH B 12 112 98 HOH HOH . 
G 6 HOH B 13 113 183 HOH HOH . 
G 6 HOH B 14 114 155 HOH HOH . 
G 6 HOH B 15 115 156 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 N N2 O72 . . . E 5 -30.208 -9.944 -2.016 1 33.81 ? N2 O72 403 A 1 
HETATM 2 N N1 O72 . . . E 5 -33.232 -9.836 -4.127 1 23.36 ? N1 O72 403 A 1 
HETATM 3 C C1 O72 . . . E 5 -32.668 -9.908 -5.342 1 22.84 ? C1 O72 403 A 1 
HETATM 4 C C2 O72 . . . E 5 -31.329 -9.987 -5.552 1 29.05 ? C2 O72 403 A 1 
HETATM 5 C C7 O72 . . . E 5 -30.99 -9.938 -3.135 1 26.11 ? C7 O72 403 A 1 
HETATM 6 C C6 O72 . . . E 5 -28.897 -9.999 -2.188 1 27.06 ? C6 O72 403 A 1 
HETATM 7 C C5 O72 . . . E 5 -28.273 -10.051 -3.419 1 24.1 ? C5 O72 403 A 1 
HETATM 8 C C4 O72 . . . E 5 -29.04 -10.062 -4.545 1 27.48 ? C4 O72 403 A 1 
HETATM 9 C C3 O72 . . . E 5 -30.448 -10.005 -4.442 1 21.73 ? C3 O72 403 A 1 
HETATM 10 N N O72 . . . E 5 -33.041 -9.702 -1.862 1 26.29 ? N O72 403 A 1 
HETATM 11 C C O72 . . . E 5 -32.433 -9.841 -3.043 1 23.32 ? C O72 403 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           11 
#