data_5RK8 # _model_server_result.job_id 5eHP7SQeG4DLBIFTeS7WeQ _model_server_result.datetime_utc '2024-11-07 22:43:33' _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 5rk8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1501}' # _entry.id 5RK8 # _exptl.entry_id 5RK8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 203.24 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(2-methyl-1H-benzimidazol-1-yl)propanamide _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 100.34 _cell.angle_gamma 90 _cell.entry_id 5RK8 _cell.length_a 81.453 _cell.length_b 26.927 _cell.length_c 55.965 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RK8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _chem_comp.formula 'C11 H13 N3 O' _chem_comp.formula_weight 203.24 _chem_comp.id UVJ _chem_comp.mon_nstd_flag . _chem_comp.name 3-(2-methyl-1H-benzimidazol-1-yl)propanamide _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 C1 UVJ sing 358 n n N C1 UVJ doub 359 n y N C2 UVJ sing 360 n y C1 N1 UVJ sing 361 n y C2 C3 UVJ doub 362 n y C2 C7 UVJ sing 363 n y C3 C4 UVJ sing 364 n y O C10 UVJ doub 365 n n N1 C7 UVJ sing 366 n y N1 C8 UVJ sing 367 n n C9 C10 UVJ sing 368 n n C9 C8 UVJ sing 369 n n C7 C6 UVJ doub 370 n y C4 C5 UVJ doub 371 n y C10 N2 UVJ sing 372 n n C6 C5 UVJ sing 373 n y C4 H1 UVJ sing 374 n n C5 H2 UVJ sing 375 n n C6 H3 UVJ sing 376 n n C8 H4 UVJ sing 377 n n C8 H5 UVJ sing 378 n n C H6 UVJ sing 379 n n C H7 UVJ sing 380 n n C H8 UVJ sing 381 n n C3 H9 UVJ sing 382 n n C9 H10 UVJ sing 383 n n C9 H11 UVJ sing 384 n n N2 H12 UVJ sing 385 n n N2 H13 UVJ sing 386 n n # _atom_sites.entry_id 5RK8 _atom_sites.fract_transf_matrix[1][1] 0.012277 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00224 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.037137 _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] 0.018163 _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 UVJ A 1 1501 1501 UVJ LIG . C 3 HOH A 1 1601 24 HOH HOH . C 3 HOH A 2 1602 195 HOH HOH . C 3 HOH A 3 1603 183 HOH HOH . C 3 HOH A 4 1604 7 HOH HOH . C 3 HOH A 5 1605 151 HOH HOH . C 3 HOH A 6 1606 197 HOH HOH . C 3 HOH A 7 1607 85 HOH HOH . C 3 HOH A 8 1608 47 HOH HOH . C 3 HOH A 9 1609 1 HOH HOH . C 3 HOH A 10 1610 17 HOH HOH . C 3 HOH A 11 1611 98 HOH HOH . C 3 HOH A 12 1612 12 HOH HOH . C 3 HOH A 13 1613 187 HOH HOH . C 3 HOH A 14 1614 89 HOH HOH . C 3 HOH A 15 1615 140 HOH HOH . C 3 HOH A 16 1616 65 HOH HOH . C 3 HOH A 17 1617 162 HOH HOH . C 3 HOH A 18 1618 160 HOH HOH . C 3 HOH A 19 1619 7 HOH HOH . C 3 HOH A 20 1620 171 HOH HOH . C 3 HOH A 21 1621 10 HOH HOH . C 3 HOH A 22 1622 84 HOH HOH . C 3 HOH A 23 1623 20 HOH HOH . C 3 HOH A 24 1624 33 HOH HOH . C 3 HOH A 25 1625 74 HOH HOH . C 3 HOH A 26 1626 145 HOH HOH . C 3 HOH A 27 1627 124 HOH HOH . C 3 HOH A 28 1628 9 HOH HOH . C 3 HOH A 29 1629 25 HOH HOH . C 3 HOH A 30 1630 76 HOH HOH . C 3 HOH A 31 1631 50 HOH HOH . C 3 HOH A 32 1632 154 HOH HOH . C 3 HOH A 33 1633 184 HOH HOH . C 3 HOH A 34 1634 54 HOH HOH . C 3 HOH A 35 1635 31 HOH HOH . C 3 HOH A 36 1636 4 HOH HOH . C 3 HOH A 37 1637 83 HOH HOH . C 3 HOH A 38 1638 66 HOH HOH . C 3 HOH A 39 1639 135 HOH HOH . C 3 HOH A 40 1640 181 HOH HOH . C 3 HOH A 41 1641 36 HOH HOH . C 3 HOH A 42 1642 179 HOH HOH . C 3 HOH A 43 1643 101 HOH HOH . C 3 HOH A 44 1644 176 HOH HOH . C 3 HOH A 45 1645 108 HOH HOH . C 3 HOH A 46 1646 64 HOH HOH . C 3 HOH A 47 1647 92 HOH HOH . C 3 HOH A 48 1648 35 HOH HOH . C 3 HOH A 49 1649 70 HOH HOH . C 3 HOH A 50 1650 3 HOH HOH . C 3 HOH A 51 1651 94 HOH HOH . C 3 HOH A 52 1652 75 HOH HOH . C 3 HOH A 53 1653 1 HOH HOH . C 3 HOH A 54 1654 56 HOH HOH . C 3 HOH A 55 1655 6 HOH HOH . C 3 HOH A 56 1656 11 HOH HOH . C 3 HOH A 57 1657 138 HOH HOH . C 3 HOH A 58 1658 182 HOH HOH . C 3 HOH A 59 1659 130 HOH HOH . C 3 HOH A 60 1660 161 HOH HOH . C 3 HOH A 61 1661 16 HOH HOH . C 3 HOH A 62 1662 62 HOH HOH . C 3 HOH A 63 1663 52 HOH HOH . C 3 HOH A 64 1664 39 HOH HOH . C 3 HOH A 65 1665 14 HOH HOH . C 3 HOH A 66 1666 60 HOH HOH . C 3 HOH A 67 1667 77 HOH HOH . C 3 HOH A 68 1668 157 HOH HOH . C 3 HOH A 69 1669 55 HOH HOH . C 3 HOH A 70 1670 178 HOH HOH . C 3 HOH A 71 1671 180 HOH HOH . C 3 HOH A 72 1672 21 HOH HOH . C 3 HOH A 73 1673 45 HOH HOH . C 3 HOH A 74 1674 59 HOH HOH . C 3 HOH A 75 1675 18 HOH HOH . C 3 HOH A 76 1676 82 HOH HOH . C 3 HOH A 77 1677 106 HOH HOH . C 3 HOH A 78 1678 139 HOH HOH . C 3 HOH A 79 1679 69 HOH HOH . C 3 HOH A 80 1680 27 HOH HOH . C 3 HOH A 81 1681 174 HOH HOH . C 3 HOH A 82 1682 71 HOH HOH . C 3 HOH A 83 1683 123 HOH HOH . C 3 HOH A 84 1684 16 HOH HOH . C 3 HOH A 85 1685 28 HOH HOH . C 3 HOH A 86 1686 207 HOH HOH . C 3 HOH A 87 1687 10 HOH HOH . C 3 HOH A 88 1688 5 HOH HOH . C 3 HOH A 89 1689 26 HOH HOH . C 3 HOH A 90 1690 128 HOH HOH . C 3 HOH A 91 1691 152 HOH HOH . C 3 HOH A 92 1692 42 HOH HOH . C 3 HOH A 93 1693 119 HOH HOH . C 3 HOH A 94 1694 127 HOH HOH . C 3 HOH A 95 1695 167 HOH HOH . C 3 HOH A 96 1696 40 HOH HOH . C 3 HOH A 97 1697 67 HOH HOH . C 3 HOH A 98 1698 91 HOH HOH . C 3 HOH A 99 1699 122 HOH HOH . C 3 HOH A 100 1700 15 HOH HOH . C 3 HOH A 101 1701 113 HOH HOH . C 3 HOH A 102 1702 23 HOH HOH . C 3 HOH A 103 1703 105 HOH HOH . C 3 HOH A 104 1704 3 HOH HOH . C 3 HOH A 105 1705 96 HOH HOH . C 3 HOH A 106 1706 90 HOH HOH . C 3 HOH A 107 1707 38 HOH HOH . C 3 HOH A 108 1708 86 HOH HOH . C 3 HOH A 109 1709 48 HOH HOH . C 3 HOH A 110 1710 88 HOH HOH . C 3 HOH A 111 1711 63 HOH HOH . C 3 HOH A 112 1712 116 HOH HOH . C 3 HOH A 113 1713 131 HOH HOH . C 3 HOH A 114 1714 19 HOH HOH . C 3 HOH A 115 1715 205 HOH HOH . C 3 HOH A 116 1716 120 HOH HOH . C 3 HOH A 117 1717 43 HOH HOH . C 3 HOH A 118 1718 29 HOH HOH . C 3 HOH A 119 1719 125 HOH HOH . C 3 HOH A 120 1720 134 HOH HOH . C 3 HOH A 121 1721 49 HOH HOH . C 3 HOH A 122 1722 150 HOH HOH . C 3 HOH A 123 1723 80 HOH HOH . C 3 HOH A 124 1724 5 HOH HOH . C 3 HOH A 125 1725 37 HOH HOH . C 3 HOH A 126 1726 206 HOH HOH . C 3 HOH A 127 1727 118 HOH HOH . C 3 HOH A 128 1728 58 HOH HOH . C 3 HOH A 129 1729 53 HOH HOH . C 3 HOH A 130 1730 72 HOH HOH . C 3 HOH A 131 1731 9 HOH HOH . C 3 HOH A 132 1732 22 HOH HOH . C 3 HOH A 133 1733 132 HOH HOH . C 3 HOH A 134 1734 133 HOH HOH . C 3 HOH A 135 1735 81 HOH HOH . C 3 HOH A 136 1736 2 HOH HOH . C 3 HOH A 137 1737 34 HOH HOH . C 3 HOH A 138 1738 117 HOH HOH . C 3 HOH A 139 1739 109 HOH HOH . C 3 HOH A 140 1740 57 HOH HOH . C 3 HOH A 141 1741 13 HOH HOH . C 3 HOH A 142 1742 146 HOH HOH . C 3 HOH A 143 1743 165 HOH HOH . C 3 HOH A 144 1744 126 HOH HOH . C 3 HOH A 145 1745 95 HOH HOH . C 3 HOH A 146 1746 158 HOH HOH . C 3 HOH A 147 1747 129 HOH HOH . C 3 HOH A 148 1748 175 HOH HOH . C 3 HOH A 149 1749 166 HOH HOH . C 3 HOH A 150 1750 149 HOH HOH . C 3 HOH A 151 1751 199 HOH HOH . C 3 HOH A 152 1752 136 HOH HOH . C 3 HOH A 153 1753 194 HOH HOH . C 3 HOH A 154 1754 115 HOH HOH . C 3 HOH A 155 1755 8 HOH HOH . C 3 HOH A 156 1756 14 HOH HOH . C 3 HOH A 157 1757 185 HOH HOH . C 3 HOH A 158 1758 114 HOH HOH . C 3 HOH A 159 1759 164 HOH HOH . C 3 HOH A 160 1760 30 HOH HOH . C 3 HOH A 161 1761 17 HOH HOH . C 3 HOH A 162 1762 112 HOH HOH . C 3 HOH A 163 1763 198 HOH HOH . C 3 HOH A 164 1764 186 HOH HOH . C 3 HOH A 165 1765 41 HOH HOH . C 3 HOH A 166 1766 61 HOH HOH . C 3 HOH A 167 1767 209 HOH HOH . C 3 HOH A 168 1768 188 HOH HOH . C 3 HOH A 169 1769 168 HOH HOH . C 3 HOH A 170 1770 170 HOH HOH . C 3 HOH A 171 1771 51 HOH HOH . C 3 HOH A 172 1772 163 HOH HOH . C 3 HOH A 173 1773 4 HOH HOH . C 3 HOH A 174 1774 190 HOH HOH . C 3 HOH A 175 1775 193 HOH HOH . C 3 HOH A 176 1776 18 HOH HOH . C 3 HOH A 177 1777 8 HOH HOH . C 3 HOH A 178 1778 110 HOH HOH . C 3 HOH A 179 1779 78 HOH HOH . C 3 HOH A 180 1780 102 HOH HOH . C 3 HOH A 181 1781 201 HOH HOH . C 3 HOH A 182 1782 68 HOH HOH . C 3 HOH A 183 1783 46 HOH HOH . C 3 HOH A 184 1784 104 HOH HOH . C 3 HOH A 185 1785 12 HOH HOH . C 3 HOH A 186 1786 2 HOH HOH . C 3 HOH A 187 1787 73 HOH HOH . C 3 HOH A 188 1788 200 HOH HOH . C 3 HOH A 189 1789 11 HOH HOH . C 3 HOH A 190 1790 15 HOH HOH . C 3 HOH A 191 1791 13 HOH HOH . C 3 HOH A 192 1792 87 HOH HOH . C 3 HOH A 193 1793 111 HOH HOH . C 3 HOH A 194 1794 93 HOH HOH . C 3 HOH A 195 1795 196 HOH HOH . C 3 HOH A 196 1796 192 HOH HOH . C 3 HOH A 197 1797 97 HOH HOH . C 3 HOH A 198 1798 203 HOH HOH . C 3 HOH A 199 1799 79 HOH HOH . C 3 HOH A 200 1800 6 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 N1 UVJ . . . B 2 -19.382 13.426 25.962 0.44 11.56 ? N1 UVJ 1501 A 1 HETATM 2 C C4 UVJ . . . B 2 -23.148 11.85 26.516 0.44 11.94 ? C4 UVJ 1501 A 1 HETATM 3 C C5 UVJ . . . B 2 -22.633 12.599 27.596 0.44 11.51 ? C5 UVJ 1501 A 1 HETATM 4 C C6 UVJ . . . B 2 -21.366 13.16 27.545 0.44 10.91 ? C6 UVJ 1501 A 1 HETATM 5 C C7 UVJ . . . B 2 -20.638 12.963 26.38 0.44 11.15 ? C7 UVJ 1501 A 1 HETATM 6 C C8 UVJ . . . B 2 -18.47 14.232 26.748 0.44 11.92 ? C8 UVJ 1501 A 1 HETATM 7 C C10 UVJ . . . B 2 -17.273 16.415 26.636 0.44 13.55 ? C10 UVJ 1501 A 1 HETATM 8 N N UVJ . . . B 2 -20.217 12.187 24.248 0.44 11.1 ? N UVJ 1501 A 1 HETATM 9 C C UVJ . . . B 2 -17.985 13.272 23.873 0.44 11.96 ? C UVJ 1501 A 1 HETATM 10 O O UVJ . . . B 2 -16.688 17.15 25.877 0.44 14 ? O UVJ 1501 A 1 HETATM 11 C C1 UVJ . . . B 2 -19.193 12.939 24.671 0.44 11.74 ? C1 UVJ 1501 A 1 HETATM 12 C C2 UVJ . . . B 2 -21.144 12.194 25.295 0.44 11.49 ? C2 UVJ 1501 A 1 HETATM 13 C C3 UVJ . . . B 2 -22.412 11.608 25.352 0.44 11.81 ? C3 UVJ 1501 A 1 HETATM 14 C C9 UVJ . . . B 2 -18.573 15.718 26.32 0.44 12.7 ? C9 UVJ 1501 A 1 HETATM 15 N N2 UVJ . . . B 2 -16.722 16.18 27.855 0.44 13.94 ? N2 UVJ 1501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 15 #