data_4P10
#
_model_server_result.job_id            rPsAM3OYZ6hUjTDiIRRMcw 
_model_server_result.datetime_utc      '2024-11-05 14:41:40' 
_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          4p10 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    4P10 
#
_exptl.entry_id    4P10 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              265.351 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid' 
_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          93.12 
_cell.angle_gamma         90 
_cell.entry_id            4P10 
_cell.length_a            49.576 
_cell.length_b            49.243 
_cell.length_c            95.048 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4P10 
_symmetry.cell_setting             . 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    Monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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                      2 
_struct_asym.id                             B 
_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
disulf ? disulf1 A SG CYS 156 A CYS 178 1_555 A SG CYS 169 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf2 A SG CYS 228 A CYS 250 1_555 A SG CYS 252 A CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
disulf ? disulf3 A SG CYS 243 A CYS 265 1_555 A SG CYS 257 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
covale ? covale1 A ND2 ASN 86 A ASN 108 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? 
metalc ? metalc1 A ND1 HIS 159 A HIS 181 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.75 ? 
metalc ? metalc2 A OE1 GLU 162 A GLU 184 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? 
metalc ? metalc3 A OE2 GLU 162 A GLU 184 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc4 A ND1 HIS 288 A HIS 310 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? 
metalc ? metalc5 B N6 2B8 . A 2B8 501 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
#
_chem_comp.formula           'C14 H23 N3 O2' 
_chem_comp.formula_weight    265.351 
_chem_comp.id                2B8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic 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
C1 C2 2B8 sing 1 n n 
C2 C3 2B8 sing 2 n n 
C3 N4 2B8 sing 3 n n 
N4 C5 2B8 sing 4 n y 
N4 C16 2B8 sing 5 n y 
C5 N6 2B8 doub 6 n y 
C15 C16 2B8 sing 7 n n 
C15 C14 2B8 sing 8 n n 
C16 C7 2B8 doub 9 n y 
O18 C17 2B8 doub 10 n n 
N6 C7 2B8 sing 11 n y 
C7 C8 2B8 sing 12 n n 
C17 O19 2B8 sing 13 n n 
C17 C9 2B8 sing 14 n n 
C14 C9 2B8 sing 15 n n 
C9 C8 2B8 sing 16 n n 
C9 C10 2B8 sing 17 n n 
C11 C10 2B8 sing 18 n n 
C11 C12 2B8 sing 19 n n 
C12 N13 2B8 sing 20 n n 
C1 H1 2B8 sing 21 n n 
C1 H2 2B8 sing 22 n n 
C1 H3 2B8 sing 23 n n 
C2 H4 2B8 sing 24 n n 
C2 H5 2B8 sing 25 n n 
C3 H6 2B8 sing 26 n n 
C3 H7 2B8 sing 27 n n 
C8 H8 2B8 sing 28 n n 
C8 H9 2B8 sing 29 n n 
C10 H10 2B8 sing 30 n n 
C10 H11 2B8 sing 31 n n 
C11 H12 2B8 sing 32 n n 
C11 H13 2B8 sing 33 n n 
C12 H14 2B8 sing 34 n n 
C12 H15 2B8 sing 35 n n 
C14 H16 2B8 sing 36 n n 
C14 H17 2B8 sing 37 n n 
C15 H18 2B8 sing 38 n n 
C15 H19 2B8 sing 39 n n 
C5 H20 2B8 sing 40 n n 
N13 H21 2B8 sing 41 n n 
N13 H22 2B8 sing 42 n n 
O19 H24 2B8 sing 43 n n 
#
_atom_sites.entry_id                     4P10 
_atom_sites.fract_transf_matrix[1][1]    0.020171 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001101 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020307 
_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]    0.010537 
_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
B 2 2B8 A 1 501 1 2B8 INH . 
C 3 ZN A 1 502 1 ZN ZN . 
D 4 DMS A 1 503 1 DMS DMS . 
E 5 NAG A 1 504 632 NAG NAG . 
F 6 HOH A 1 601 59 HOH HOH . 
F 6 HOH A 2 602 212 HOH HOH . 
F 6 HOH A 3 603 106 HOH HOH . 
F 6 HOH A 4 604 210 HOH HOH . 
F 6 HOH A 5 605 168 HOH HOH . 
F 6 HOH A 6 606 23 HOH HOH . 
F 6 HOH A 7 607 216 HOH HOH . 
F 6 HOH A 8 608 25 HOH HOH . 
F 6 HOH A 9 609 79 HOH HOH . 
F 6 HOH A 10 610 43 HOH HOH . 
F 6 HOH A 11 611 52 HOH HOH . 
F 6 HOH A 12 612 36 HOH HOH . 
F 6 HOH A 13 613 139 HOH HOH . 
F 6 HOH A 14 614 15 HOH HOH . 
F 6 HOH A 15 615 84 HOH HOH . 
F 6 HOH A 16 616 38 HOH HOH . 
F 6 HOH A 17 617 69 HOH HOH . 
F 6 HOH A 18 618 63 HOH HOH . 
F 6 HOH A 19 619 68 HOH HOH . 
F 6 HOH A 20 620 180 HOH HOH . 
F 6 HOH A 21 621 111 HOH HOH . 
F 6 HOH A 22 622 208 HOH HOH . 
F 6 HOH A 23 623 5 HOH HOH . 
F 6 HOH A 24 624 203 HOH HOH . 
F 6 HOH A 25 625 2 HOH HOH . 
F 6 HOH A 26 626 3 HOH HOH . 
F 6 HOH A 27 627 4 HOH HOH . 
F 6 HOH A 28 628 6 HOH HOH . 
F 6 HOH A 29 629 7 HOH HOH . 
F 6 HOH A 30 630 8 HOH HOH . 
F 6 HOH A 31 631 9 HOH HOH . 
F 6 HOH A 32 632 10 HOH HOH . 
F 6 HOH A 33 633 11 HOH HOH . 
F 6 HOH A 34 634 12 HOH HOH . 
F 6 HOH A 35 635 13 HOH HOH . 
F 6 HOH A 36 636 14 HOH HOH . 
F 6 HOH A 37 637 16 HOH HOH . 
F 6 HOH A 38 638 17 HOH HOH . 
F 6 HOH A 39 639 18 HOH HOH . 
F 6 HOH A 40 640 19 HOH HOH . 
F 6 HOH A 41 641 20 HOH HOH . 
F 6 HOH A 42 642 21 HOH HOH . 
F 6 HOH A 43 643 22 HOH HOH . 
F 6 HOH A 44 644 24 HOH HOH . 
F 6 HOH A 45 645 26 HOH HOH . 
F 6 HOH A 46 646 27 HOH HOH . 
F 6 HOH A 47 647 28 HOH HOH . 
F 6 HOH A 48 648 29 HOH HOH . 
F 6 HOH A 49 649 31 HOH HOH . 
F 6 HOH A 50 650 32 HOH HOH . 
F 6 HOH A 51 651 33 HOH HOH . 
F 6 HOH A 52 652 34 HOH HOH . 
F 6 HOH A 53 653 35 HOH HOH . 
F 6 HOH A 54 654 37 HOH HOH . 
F 6 HOH A 55 655 39 HOH HOH . 
F 6 HOH A 56 656 40 HOH HOH . 
F 6 HOH A 57 657 41 HOH HOH . 
F 6 HOH A 58 658 42 HOH HOH . 
F 6 HOH A 59 659 44 HOH HOH . 
F 6 HOH A 60 660 45 HOH HOH . 
F 6 HOH A 61 661 46 HOH HOH . 
F 6 HOH A 62 662 47 HOH HOH . 
F 6 HOH A 63 663 48 HOH HOH . 
F 6 HOH A 64 664 49 HOH HOH . 
F 6 HOH A 65 665 50 HOH HOH . 
F 6 HOH A 66 666 53 HOH HOH . 
F 6 HOH A 67 667 54 HOH HOH . 
F 6 HOH A 68 668 55 HOH HOH . 
F 6 HOH A 69 669 57 HOH HOH . 
F 6 HOH A 70 670 58 HOH HOH . 
F 6 HOH A 71 671 61 HOH HOH . 
F 6 HOH A 72 672 64 HOH HOH . 
F 6 HOH A 73 673 67 HOH HOH . 
F 6 HOH A 74 674 70 HOH HOH . 
F 6 HOH A 75 675 71 HOH HOH . 
F 6 HOH A 76 676 72 HOH HOH . 
F 6 HOH A 77 677 73 HOH HOH . 
F 6 HOH A 78 678 74 HOH HOH . 
F 6 HOH A 79 679 75 HOH HOH . 
F 6 HOH A 80 680 76 HOH HOH . 
F 6 HOH A 81 681 77 HOH HOH . 
F 6 HOH A 82 682 78 HOH HOH . 
F 6 HOH A 83 683 80 HOH HOH . 
F 6 HOH A 84 684 81 HOH HOH . 
F 6 HOH A 85 685 82 HOH HOH . 
F 6 HOH A 86 686 83 HOH HOH . 
F 6 HOH A 87 687 85 HOH HOH . 
F 6 HOH A 88 688 86 HOH HOH . 
F 6 HOH A 89 689 87 HOH HOH . 
F 6 HOH A 90 690 88 HOH HOH . 
F 6 HOH A 91 691 89 HOH HOH . 
F 6 HOH A 92 692 90 HOH HOH . 
F 6 HOH A 93 693 91 HOH HOH . 
F 6 HOH A 94 694 92 HOH HOH . 
F 6 HOH A 95 695 93 HOH HOH . 
F 6 HOH A 96 696 94 HOH HOH . 
F 6 HOH A 97 697 95 HOH HOH . 
F 6 HOH A 98 698 100 HOH HOH . 
F 6 HOH A 99 699 101 HOH HOH . 
F 6 HOH A 100 700 102 HOH HOH . 
F 6 HOH A 101 701 103 HOH HOH . 
F 6 HOH A 102 702 107 HOH HOH . 
F 6 HOH A 103 703 108 HOH HOH . 
F 6 HOH A 104 704 110 HOH HOH . 
F 6 HOH A 105 705 113 HOH HOH . 
F 6 HOH A 106 706 114 HOH HOH . 
F 6 HOH A 107 707 118 HOH HOH . 
F 6 HOH A 108 708 119 HOH HOH . 
F 6 HOH A 109 709 120 HOH HOH . 
F 6 HOH A 110 710 121 HOH HOH . 
F 6 HOH A 111 711 123 HOH HOH . 
F 6 HOH A 112 712 126 HOH HOH . 
F 6 HOH A 113 713 127 HOH HOH . 
F 6 HOH A 114 714 128 HOH HOH . 
F 6 HOH A 115 715 131 HOH HOH . 
F 6 HOH A 116 716 132 HOH HOH . 
F 6 HOH A 117 717 134 HOH HOH . 
F 6 HOH A 118 718 137 HOH HOH . 
F 6 HOH A 119 719 141 HOH HOH . 
F 6 HOH A 120 720 144 HOH HOH . 
F 6 HOH A 121 721 145 HOH HOH . 
F 6 HOH A 122 722 146 HOH HOH . 
F 6 HOH A 123 723 147 HOH HOH . 
F 6 HOH A 124 724 148 HOH HOH . 
F 6 HOH A 125 725 153 HOH HOH . 
F 6 HOH A 126 726 157 HOH HOH . 
F 6 HOH A 127 727 159 HOH HOH . 
F 6 HOH A 128 728 163 HOH HOH . 
F 6 HOH A 129 729 166 HOH HOH . 
F 6 HOH A 130 730 169 HOH HOH . 
F 6 HOH A 131 731 173 HOH HOH . 
F 6 HOH A 132 732 178 HOH HOH . 
F 6 HOH A 133 733 182 HOH HOH . 
F 6 HOH A 134 734 183 HOH HOH . 
F 6 HOH A 135 735 184 HOH HOH . 
F 6 HOH A 136 736 185 HOH HOH . 
F 6 HOH A 137 737 188 HOH HOH . 
F 6 HOH A 138 738 190 HOH HOH . 
F 6 HOH A 139 739 195 HOH HOH . 
F 6 HOH A 140 740 199 HOH HOH . 
F 6 HOH A 141 741 205 HOH HOH . 
F 6 HOH A 142 742 209 HOH HOH . 
F 6 HOH A 143 743 217 HOH HOH . 
F 6 HOH A 144 744 220 HOH HOH . 
F 6 HOH A 145 745 221 HOH HOH . 
F 6 HOH A 146 746 223 HOH HOH . 
F 6 HOH A 147 747 227 HOH HOH . 
F 6 HOH A 148 748 234 HOH HOH . 
F 6 HOH A 149 749 237 HOH HOH . 
F 6 HOH A 150 750 239 HOH HOH . 
F 6 HOH A 151 751 240 HOH HOH . 
F 6 HOH A 152 752 241 HOH HOH . 
F 6 HOH A 153 753 242 HOH HOH . 
F 6 HOH A 154 754 243 HOH HOH . 
F 6 HOH A 155 755 247 HOH HOH . 
F 6 HOH A 156 756 256 HOH HOH . 
F 6 HOH A 157 757 264 HOH HOH . 
F 6 HOH A 158 758 271 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 C1 2B8 . . . B 2 21.188 -3.226 16.442 1 22.66 ? C1 2B8 501 A 1 
HETATM 2 C C2 2B8 . . . B 2 20.76 -2.284 17.567 1 21.41 ? C2 2B8 501 A 1 
HETATM 3 C C3 2B8 . . . B 2 21.968 -1.902 18.369 1 16.82 ? C3 2B8 501 A 1 
HETATM 4 N N6 2B8 . . . B 2 20.642 -0.168 21.249 1 20.05 ? N6 2B8 501 A 1 
HETATM 5 C C7 2B8 . . . B 2 21.95 -0.122 21.53 1 18.79 ? C7 2B8 501 A 1 
HETATM 6 C C8 2B8 . . . B 2 22.505 0.481 22.753 1 19.03 ? C8 2B8 501 A 1 
HETATM 7 C C9 2B8 . . . B 2 24.024 0.632 22.529 1 18.43 ? C9 2B8 501 A 1 
HETATM 8 C C10 2B8 . . . B 2 24.717 0.891 23.91 1 17.26 ? C10 2B8 501 A 1 
HETATM 9 C C11 2B8 . . . B 2 26.14 1.415 23.814 1 16.73 ? C11 2B8 501 A 1 
HETATM 10 C C12 2B8 . . . B 2 26.85 1.499 25.218 1 20.02 ? C12 2B8 501 A 1 
HETATM 11 C C14 2B8 . . . B 2 24.71 -0.586 21.827 1 19.18 ? C14 2B8 501 A 1 
HETATM 12 C C15 2B8 . . . B 2 24.087 -0.927 20.446 1 18.21 ? C15 2B8 501 A 1 
HETATM 13 C C16 2B8 . . . B 2 22.648 -0.751 20.534 1 17.98 ? C16 2B8 501 A 1 
HETATM 14 N N4 2B8 . . . B 2 21.699 -1.178 19.623 1 19.73 ? N4 2B8 501 A 1 
HETATM 15 C C5 2B8 . . . B 2 20.465 -0.821 20.105 1 18.72 ? C5 2B8 501 A 1 
HETATM 16 N N13 2B8 . . . B 2 26.152 2.558 26.077 1 18.31 ? N13 2B8 501 A 1 
HETATM 17 C C17 2B8 . . . B 2 24.178 1.914 21.706 1 18.43 ? C17 2B8 501 A 1 
HETATM 18 O O18 2B8 . . . B 2 24.847 2.088 20.703 1 17.76 ? O18 2B8 501 A 1 
HETATM 19 O O19 2B8 . . . B 2 23.471 2.963 22.168 1 19.73 ? O19 2B8 501 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#