data_3LP1
#
_model_server_result.job_id            DvQ3UmTajTBIKbbnGq-AJQ 
_model_server_result.datetime_utc      '2024-11-14 18:01:28' 
_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          3lp1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    3LP1 
#
_exptl.entry_id    3LP1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              246.262 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one 
_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            3LP1 
_cell.length_a            118.784 
_cell.length_b            155.264 
_cell.length_c            155.244 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LP1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 tetrameric 4 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,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 77.622 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 A OD1 ASP 446 A ASP 443 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc2 A OD2 ASP 446 A ASP 443 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc3 A OE2 GLU 481 A GLU 478 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 A OD1 ASP 501 A ASP 498 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc5 A OD1 ASP 552 A ASP 549 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc6 C O LP8 . A LP8 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc7 C O3 LP8 . A LP8 601 1_555 D MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc8 C O LP8 . A LP8 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc9 C N9 LP8 . A LP8 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
#
_chem_comp.formula           'C13 H14 N2 O3' 
_chem_comp.formula_weight    246.262 
_chem_comp.id                LP8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one 
_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
C C2 LP8 sing 194 n n 
C O3 LP8 doub 195 n n 
N C LP8 sing 196 n n 
O N LP8 sing 197 n n 
O HO LP8 sing 198 n n 
C1 C2 LP8 doub 199 n n 
C2 C11 LP8 sing 200 n n 
C4 N LP8 sing 201 n n 
C4 C5 LP8 doub 202 n y 
C5 C1 LP8 sing 203 n n 
C6 C5 LP8 sing 204 n y 
C6 H6 LP8 sing 205 n n 
C7 C6 LP8 doub 206 n y 
C7 H7 LP8 sing 207 n n 
C8 C7 LP8 sing 208 n y 
C8 N9 LP8 doub 209 n y 
C8 H8 LP8 sing 210 n n 
N9 C4 LP8 sing 211 n y 
O10 C1 LP8 sing 212 n n 
O10 H151 LP8 sing 213 n n 
C11 C12 LP8 sing 214 n n 
C11 H11 LP8 sing 215 n n 
C12 C13 LP8 sing 216 n n 
C12 H12 LP8 sing 217 n n 
C12 H12A LP8 sing 218 n n 
C13 H13 LP8 sing 219 n n 
C13 H13A LP8 sing 220 n n 
C14 C13 LP8 sing 221 n n 
C14 H14 LP8 sing 222 n n 
C14 H14A LP8 sing 223 n n 
C15 C11 LP8 sing 224 n n 
C15 C14 LP8 sing 225 n n 
C15 H15 LP8 sing 226 n n 
C15 H15A LP8 sing 227 n n 
#
_atom_sites.entry_id                     3LP1 
_atom_sites.fract_transf_matrix[1][1]    0.008419 
_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]    0.006441 
_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]    0.006441 
_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 LP8 A 1 601 601 LP8 LP8 . 
D 4 MN A 1 602 602 MN MN . 
E 4 MN A 1 603 603 MN MN . 
F 5 NVP A 1 701 701 NVP NVP . 
G 6 HOH A 1 561 2 HOH HOH . 
G 6 HOH A 2 562 3 HOH HOH . 
G 6 HOH A 3 563 5 HOH HOH . 
G 6 HOH A 4 564 6 HOH HOH . 
G 6 HOH A 5 565 7 HOH HOH . 
G 6 HOH A 6 566 8 HOH HOH . 
G 6 HOH A 7 567 9 HOH HOH . 
G 6 HOH A 8 568 10 HOH HOH . 
G 6 HOH A 9 569 11 HOH HOH . 
G 6 HOH A 10 570 13 HOH HOH . 
G 6 HOH A 11 571 14 HOH HOH . 
G 6 HOH A 12 572 15 HOH HOH . 
G 6 HOH A 13 573 16 HOH HOH . 
G 6 HOH A 14 574 17 HOH HOH . 
G 6 HOH A 15 575 19 HOH HOH . 
G 6 HOH A 16 576 22 HOH HOH . 
G 6 HOH A 17 577 24 HOH HOH . 
G 6 HOH A 18 578 25 HOH HOH . 
G 6 HOH A 19 579 26 HOH HOH . 
G 6 HOH A 20 580 29 HOH HOH . 
G 6 HOH A 21 581 31 HOH HOH . 
G 6 HOH A 22 582 32 HOH HOH . 
G 6 HOH A 23 583 36 HOH HOH . 
G 6 HOH A 24 584 37 HOH HOH . 
G 6 HOH A 25 585 38 HOH HOH . 
G 6 HOH A 26 586 41 HOH HOH . 
G 6 HOH A 27 587 43 HOH HOH . 
G 6 HOH A 28 588 44 HOH HOH . 
G 6 HOH A 29 589 45 HOH HOH . 
G 6 HOH A 30 590 46 HOH HOH . 
G 6 HOH A 31 591 49 HOH HOH . 
G 6 HOH A 32 592 50 HOH HOH . 
G 6 HOH A 33 593 51 HOH HOH . 
G 6 HOH A 34 594 52 HOH HOH . 
G 6 HOH A 35 595 53 HOH HOH . 
G 6 HOH A 36 596 57 HOH HOH . 
G 6 HOH A 37 597 63 HOH HOH . 
G 6 HOH A 38 598 64 HOH HOH . 
G 6 HOH A 39 599 67 HOH HOH . 
G 6 HOH A 40 600 72 HOH HOH . 
G 6 HOH A 41 604 73 HOH HOH . 
G 6 HOH A 42 605 76 HOH HOH . 
G 6 HOH A 43 606 77 HOH HOH . 
G 6 HOH A 44 607 80 HOH HOH . 
G 6 HOH A 45 608 81 HOH HOH . 
G 6 HOH A 46 609 82 HOH HOH . 
G 6 HOH A 47 610 84 HOH HOH . 
G 6 HOH A 48 611 86 HOH HOH . 
G 6 HOH A 49 612 87 HOH HOH . 
G 6 HOH A 50 613 88 HOH HOH . 
G 6 HOH A 51 614 90 HOH HOH . 
G 6 HOH A 52 615 92 HOH HOH . 
G 6 HOH A 53 616 93 HOH HOH . 
G 6 HOH A 54 617 97 HOH HOH . 
G 6 HOH A 55 618 98 HOH HOH . 
G 6 HOH A 56 619 100 HOH HOH . 
G 6 HOH A 57 620 102 HOH HOH . 
G 6 HOH A 58 621 103 HOH HOH . 
G 6 HOH A 59 622 104 HOH HOH . 
G 6 HOH A 60 623 105 HOH HOH . 
G 6 HOH A 61 624 106 HOH HOH . 
G 6 HOH A 62 625 107 HOH HOH . 
G 6 HOH A 63 626 108 HOH HOH . 
G 6 HOH A 64 627 109 HOH HOH . 
G 6 HOH A 65 628 111 HOH HOH . 
G 6 HOH A 66 629 113 HOH HOH . 
G 6 HOH A 67 630 114 HOH HOH . 
G 6 HOH A 68 631 115 HOH HOH . 
G 6 HOH A 69 632 116 HOH HOH . 
G 6 HOH A 70 633 117 HOH HOH . 
G 6 HOH A 71 634 118 HOH HOH . 
G 6 HOH A 72 635 120 HOH HOH . 
G 6 HOH A 73 636 121 HOH HOH . 
G 6 HOH A 74 637 123 HOH HOH . 
G 6 HOH A 75 638 124 HOH HOH . 
G 6 HOH A 76 639 125 HOH HOH . 
G 6 HOH A 77 640 127 HOH HOH . 
G 6 HOH A 78 641 129 HOH HOH . 
G 6 HOH A 79 642 130 HOH HOH . 
G 6 HOH A 80 643 133 HOH HOH . 
G 6 HOH A 81 644 134 HOH HOH . 
G 6 HOH A 82 645 135 HOH HOH . 
G 6 HOH A 83 646 136 HOH HOH . 
G 6 HOH A 84 647 139 HOH HOH . 
G 6 HOH A 85 648 141 HOH HOH . 
G 6 HOH A 86 649 142 HOH HOH . 
G 6 HOH A 87 650 145 HOH HOH . 
G 6 HOH A 88 651 146 HOH HOH . 
G 6 HOH A 89 652 147 HOH HOH . 
G 6 HOH A 90 653 149 HOH HOH . 
G 6 HOH A 91 654 151 HOH HOH . 
G 6 HOH A 92 655 152 HOH HOH . 
G 6 HOH A 93 656 157 HOH HOH . 
G 6 HOH A 94 657 158 HOH HOH . 
G 6 HOH A 95 658 160 HOH HOH . 
G 6 HOH A 96 659 161 HOH HOH . 
G 6 HOH A 97 660 164 HOH HOH . 
G 6 HOH A 98 661 166 HOH HOH . 
G 6 HOH A 99 662 167 HOH HOH . 
G 6 HOH A 100 663 168 HOH HOH . 
G 6 HOH A 101 664 169 HOH HOH . 
G 6 HOH A 102 665 170 HOH HOH . 
G 6 HOH A 103 666 171 HOH HOH . 
G 6 HOH A 104 667 172 HOH HOH . 
G 6 HOH A 105 668 173 HOH HOH . 
G 6 HOH A 106 669 174 HOH HOH . 
G 6 HOH A 107 670 175 HOH HOH . 
G 6 HOH A 108 671 150 HOH HOH . 
H 6 HOH B 1 441 1 HOH HOH . 
H 6 HOH B 2 442 4 HOH HOH . 
H 6 HOH B 3 443 12 HOH HOH . 
H 6 HOH B 4 444 18 HOH HOH . 
H 6 HOH B 5 445 20 HOH HOH . 
H 6 HOH B 6 446 21 HOH HOH . 
H 6 HOH B 7 447 23 HOH HOH . 
H 6 HOH B 8 448 27 HOH HOH . 
H 6 HOH B 9 449 28 HOH HOH . 
H 6 HOH B 10 450 30 HOH HOH . 
H 6 HOH B 11 451 33 HOH HOH . 
H 6 HOH B 12 452 34 HOH HOH . 
H 6 HOH B 13 453 35 HOH HOH . 
H 6 HOH B 14 454 39 HOH HOH . 
H 6 HOH B 15 455 40 HOH HOH . 
H 6 HOH B 16 456 42 HOH HOH . 
H 6 HOH B 17 457 47 HOH HOH . 
H 6 HOH B 18 458 48 HOH HOH . 
H 6 HOH B 19 459 54 HOH HOH . 
H 6 HOH B 20 460 55 HOH HOH . 
H 6 HOH B 21 461 56 HOH HOH . 
H 6 HOH B 22 462 58 HOH HOH . 
H 6 HOH B 23 463 59 HOH HOH . 
H 6 HOH B 24 464 60 HOH HOH . 
H 6 HOH B 25 465 61 HOH HOH . 
H 6 HOH B 26 466 62 HOH HOH . 
H 6 HOH B 27 467 65 HOH HOH . 
H 6 HOH B 28 468 66 HOH HOH . 
H 6 HOH B 29 469 68 HOH HOH . 
H 6 HOH B 30 470 69 HOH HOH . 
H 6 HOH B 31 471 70 HOH HOH . 
H 6 HOH B 32 472 71 HOH HOH . 
H 6 HOH B 33 473 74 HOH HOH . 
H 6 HOH B 34 474 75 HOH HOH . 
H 6 HOH B 35 475 78 HOH HOH . 
H 6 HOH B 36 476 79 HOH HOH . 
H 6 HOH B 37 477 83 HOH HOH . 
H 6 HOH B 38 478 85 HOH HOH . 
H 6 HOH B 39 479 89 HOH HOH . 
H 6 HOH B 40 480 91 HOH HOH . 
H 6 HOH B 41 481 94 HOH HOH . 
H 6 HOH B 42 482 95 HOH HOH . 
H 6 HOH B 43 483 96 HOH HOH . 
H 6 HOH B 44 484 99 HOH HOH . 
H 6 HOH B 45 485 101 HOH HOH . 
H 6 HOH B 46 486 110 HOH HOH . 
H 6 HOH B 47 487 112 HOH HOH . 
H 6 HOH B 48 488 119 HOH HOH . 
H 6 HOH B 49 489 122 HOH HOH . 
H 6 HOH B 50 490 126 HOH HOH . 
H 6 HOH B 51 491 128 HOH HOH . 
H 6 HOH B 52 492 131 HOH HOH . 
H 6 HOH B 53 493 132 HOH HOH . 
H 6 HOH B 54 494 137 HOH HOH . 
H 6 HOH B 55 495 138 HOH HOH . 
H 6 HOH B 56 496 140 HOH HOH . 
H 6 HOH B 57 497 143 HOH HOH . 
H 6 HOH B 58 498 144 HOH HOH . 
H 6 HOH B 59 499 148 HOH HOH . 
H 6 HOH B 60 501 153 HOH HOH . 
H 6 HOH B 61 502 154 HOH HOH . 
H 6 HOH B 62 503 155 HOH HOH . 
H 6 HOH B 63 504 156 HOH HOH . 
H 6 HOH B 64 505 159 HOH HOH . 
H 6 HOH B 65 506 162 HOH HOH . 
H 6 HOH B 66 507 163 HOH HOH . 
H 6 HOH B 67 508 165 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 C LP8 . . . C 3 -3.677 74.27 34.267 1 44.94 ? C LP8 601 A 1 
HETATM 2 N N LP8 . . . C 3 -4.166 73.339 33.411 1 44.95 ? N LP8 601 A 1 
HETATM 3 O O LP8 . . . C 3 -5.548 73.228 33.313 1 44.95 ? O LP8 601 A 1 
HETATM 4 C C1 LP8 . . . C 3 -1.493 73.522 33.585 1 44.97 ? C1 LP8 601 A 1 
HETATM 5 C C2 LP8 . . . C 3 -2.28 74.379 34.366 1 45 ? C2 LP8 601 A 1 
HETATM 6 O O3 LP8 . . . C 3 -4.498 75.045 34.975 1 44.82 ? O3 LP8 601 A 1 
HETATM 7 C C4 LP8 . . . C 3 -3.452 72.491 32.635 1 44.98 ? C4 LP8 601 A 1 
HETATM 8 C C5 LP8 . . . C 3 -2.061 72.583 32.723 1 45.02 ? C5 LP8 601 A 1 
HETATM 9 C C6 LP8 . . . C 3 -1.315 71.714 31.925 1 44.89 ? C6 LP8 601 A 1 
HETATM 10 C C7 LP8 . . . C 3 -1.942 70.798 31.083 1 44.94 ? C7 LP8 601 A 1 
HETATM 11 C C8 LP8 . . . C 3 -3.334 70.784 31.069 1 44.91 ? C8 LP8 601 A 1 
HETATM 12 N N9 LP8 . . . C 3 -4.092 71.611 31.827 1 44.99 ? N9 LP8 601 A 1 
HETATM 13 O O10 LP8 . . . C 3 -0.161 73.511 33.581 1 44.92 ? O10 LP8 601 A 1 
HETATM 14 C C11 LP8 . . . C 3 -1.732 75.416 35.331 1 44.98 ? C11 LP8 601 A 1 
HETATM 15 C C12 LP8 . . . C 3 -1.259 74.86 36.678 1 45.22 ? C12 LP8 601 A 1 
HETATM 16 C C13 LP8 . . . C 3 0.147 75.415 36.906 1 45.2 ? C13 LP8 601 A 1 
HETATM 17 C C14 LP8 . . . C 3 0.191 76.69 36.062 1 45.14 ? C14 LP8 601 A 1 
HETATM 18 C C15 LP8 . . . C 3 -0.596 76.304 34.807 1 45.06 ? C15 LP8 601 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#