data_5DKD
#
_model_server_result.job_id            TfXTFY17QxCJTfI1kXGfuw 
_model_server_result.datetime_utc      '2025-01-10 22:50:11' 
_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          5dkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1605}' 
#
_entry.id    5DKD 
#
_exptl.entry_id    5DKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              321.373 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.9 
_cell.angle_gamma         90 
_cell.entry_id            5DKD 
_cell.length_a            45.926 
_cell.length_b            74.566 
_cell.length_c            52.626 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,M 1 1 
B,H,I,J,K,L,N 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 G N N 
? 4 L N 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 ND1 HIS 69 A HIS 1517 1_555 C ZN ZN . A ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc2 C ZN ZN . A ZN 1601 1_555 M O HOH . A HOH 1740 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc3 C ZN ZN . A ZN 1601 1_555 N O HOH . B HOH 1712 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc4 C ZN ZN . A ZN 1601 1_555 N O HOH . B HOH 1719 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc5 C ZN ZN . A ZN 1601 1_555 N O HOH . B HOH 1723 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc6 C ZN ZN . A ZN 1601 1_555 N O HOH . B HOH 1747 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc7 M O HOH . A HOH 1709 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc8 M O HOH . A HOH 1714 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc9 M O HOH . A HOH 1735 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
metalc ? metalc10 M O HOH . A HOH 1750 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc11 B ND1 HIS 69 B HIS 1517 1_555 H ZN ZN . B ZN 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc12 H ZN ZN . B ZN 1601 1_555 N O HOH . B HOH 1741 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
#
_chem_comp.formula           'C19 H19 N3 O2' 
_chem_comp.formula_weight    321.373 
_chem_comp.id                5BW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-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
CAA CAB 5BW doub 1 n y 
CAA CAF 5BW sing 2 n y 
CAB CAC 5BW sing 3 n y 
CAT CAU 5BW doub 4 n y 
CAT NAS 5BW sing 5 n y 
CAF CAE 5BW doub 6 n y 
CAC CAD 5BW doub 7 n y 
CAU CAV 5BW sing 8 n y 
NAS CAR 5BW doub 9 n y 
CAE CAD 5BW sing 10 n y 
CAE CAG 5BW sing 11 n n 
CAD OAJ 5BW sing 12 n n 
CAV CAW 5BW doub 13 n y 
CAQ CAP 5BW sing 14 n n 
CAQ NAL 5BW sing 15 n n 
CAR CAW 5BW sing 16 n y 
CAR NAO 5BW sing 17 n n 
CAH CAG 5BW sing 18 n n 
CAH CAK 5BW doub 19 e n 
CAG OAI 5BW doub 20 n n 
CAP NAO 5BW sing 21 n n 
CAP CAX 5BW sing 22 n n 
NAO CAN 5BW sing 23 n n 
NAL CAK 5BW sing 24 n n 
NAL CAM 5BW sing 25 n n 
CAX CAM 5BW sing 26 n n 
CAN CAM 5BW sing 27 n n 
CAW H1 5BW sing 28 n n 
CAV H2 5BW sing 29 n n 
CAU H3 5BW sing 30 n n 
CAT H4 5BW sing 31 n n 
CAN H5 5BW sing 32 n n 
CAN H6 5BW sing 33 n n 
CAM H7 5BW sing 34 n n 
CAX H8 5BW sing 35 n n 
CAX H9 5BW sing 36 n n 
CAP H10 5BW sing 37 n n 
CAQ H11 5BW sing 38 n n 
CAQ H12 5BW sing 39 n n 
CAK H13 5BW sing 40 n n 
CAH H14 5BW sing 41 n n 
CAF H15 5BW sing 42 n n 
CAA H16 5BW sing 43 n n 
CAB H17 5BW sing 44 n n 
CAC H18 5BW sing 45 n n 
OAJ H19 5BW sing 46 n n 
#
_atom_sites.entry_id                     5DKD 
_atom_sites.fract_transf_matrix[1][1]    0.021774 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00788 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013411 
_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]    0.020208 
_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 2 ZN A 1 1601 2 ZN ZN . 
D 3 EDO A 1 1602 1 EDO EDO . 
E 3 EDO A 1 1603 5 EDO EDO . 
F 3 EDO A 1 1604 6 EDO EDO . 
G 4 5BW A 1 1605 1 5BW DRG . 
H 2 ZN B 1 1601 1 ZN ZN . 
I 3 EDO B 1 1602 2 EDO EDO . 
J 3 EDO B 1 1603 3 EDO EDO . 
K 3 EDO B 1 1604 4 EDO EDO . 
L 4 5BW B 1 1605 2 5BW DRG . 
M 5 HOH A 1 1701 68 HOH HOH . 
M 5 HOH A 2 1702 69 HOH HOH . 
M 5 HOH A 3 1703 15 HOH HOH . 
M 5 HOH A 4 1704 94 HOH HOH . 
M 5 HOH A 5 1705 18 HOH HOH . 
M 5 HOH A 6 1706 24 HOH HOH . 
M 5 HOH A 7 1707 37 HOH HOH . 
M 5 HOH A 8 1708 82 HOH HOH . 
M 5 HOH A 9 1709 72 HOH HOH . 
M 5 HOH A 10 1710 35 HOH HOH . 
M 5 HOH A 11 1711 14 HOH HOH . 
M 5 HOH A 12 1712 30 HOH HOH . 
M 5 HOH A 13 1713 93 HOH HOH . 
M 5 HOH A 14 1714 22 HOH HOH . 
M 5 HOH A 15 1715 20 HOH HOH . 
M 5 HOH A 16 1716 2 HOH HOH . 
M 5 HOH A 17 1717 39 HOH HOH . 
M 5 HOH A 18 1718 25 HOH HOH . 
M 5 HOH A 19 1719 95 HOH HOH . 
M 5 HOH A 20 1720 10 HOH HOH . 
M 5 HOH A 21 1721 38 HOH HOH . 
M 5 HOH A 22 1722 17 HOH HOH . 
M 5 HOH A 23 1723 7 HOH HOH . 
M 5 HOH A 24 1724 5 HOH HOH . 
M 5 HOH A 25 1725 6 HOH HOH . 
M 5 HOH A 26 1726 4 HOH HOH . 
M 5 HOH A 27 1727 3 HOH HOH . 
M 5 HOH A 28 1728 80 HOH HOH . 
M 5 HOH A 29 1729 21 HOH HOH . 
M 5 HOH A 30 1730 60 HOH HOH . 
M 5 HOH A 31 1731 70 HOH HOH . 
M 5 HOH A 32 1732 92 HOH HOH . 
M 5 HOH A 33 1733 79 HOH HOH . 
M 5 HOH A 34 1734 45 HOH HOH . 
M 5 HOH A 35 1735 54 HOH HOH . 
M 5 HOH A 36 1736 71 HOH HOH . 
M 5 HOH A 37 1737 31 HOH HOH . 
M 5 HOH A 38 1738 96 HOH HOH . 
M 5 HOH A 39 1739 13 HOH HOH . 
M 5 HOH A 40 1740 78 HOH HOH . 
M 5 HOH A 41 1741 90 HOH HOH . 
M 5 HOH A 42 1742 85 HOH HOH . 
M 5 HOH A 43 1743 27 HOH HOH . 
M 5 HOH A 44 1744 47 HOH HOH . 
M 5 HOH A 45 1745 84 HOH HOH . 
M 5 HOH A 46 1746 43 HOH HOH . 
M 5 HOH A 47 1747 44 HOH HOH . 
M 5 HOH A 48 1748 75 HOH HOH . 
M 5 HOH A 49 1749 66 HOH HOH . 
M 5 HOH A 50 1750 73 HOH HOH . 
M 5 HOH A 51 1751 67 HOH HOH . 
M 5 HOH A 52 1752 74 HOH HOH . 
N 5 HOH B 1 1701 61 HOH HOH . 
N 5 HOH B 2 1702 57 HOH HOH . 
N 5 HOH B 3 1703 89 HOH HOH . 
N 5 HOH B 4 1704 51 HOH HOH . 
N 5 HOH B 5 1705 50 HOH HOH . 
N 5 HOH B 6 1706 12 HOH HOH . 
N 5 HOH B 7 1707 9 HOH HOH . 
N 5 HOH B 8 1708 1 HOH HOH . 
N 5 HOH B 9 1709 8 HOH HOH . 
N 5 HOH B 10 1710 49 HOH HOH . 
N 5 HOH B 11 1711 81 HOH HOH . 
N 5 HOH B 12 1712 77 HOH HOH . 
N 5 HOH B 13 1713 23 HOH HOH . 
N 5 HOH B 14 1714 28 HOH HOH . 
N 5 HOH B 15 1715 36 HOH HOH . 
N 5 HOH B 16 1716 53 HOH HOH . 
N 5 HOH B 17 1717 26 HOH HOH . 
N 5 HOH B 18 1718 19 HOH HOH . 
N 5 HOH B 19 1719 76 HOH HOH . 
N 5 HOH B 20 1720 52 HOH HOH . 
N 5 HOH B 21 1721 11 HOH HOH . 
N 5 HOH B 22 1722 29 HOH HOH . 
N 5 HOH B 23 1723 56 HOH HOH . 
N 5 HOH B 24 1724 59 HOH HOH . 
N 5 HOH B 25 1725 32 HOH HOH . 
N 5 HOH B 26 1726 88 HOH HOH . 
N 5 HOH B 27 1727 100 HOH HOH . 
N 5 HOH B 28 1728 64 HOH HOH . 
N 5 HOH B 29 1729 91 HOH HOH . 
N 5 HOH B 30 1730 101 HOH HOH . 
N 5 HOH B 31 1731 42 HOH HOH . 
N 5 HOH B 32 1732 58 HOH HOH . 
N 5 HOH B 33 1733 16 HOH HOH . 
N 5 HOH B 34 1734 83 HOH HOH . 
N 5 HOH B 35 1735 86 HOH HOH . 
N 5 HOH B 36 1736 87 HOH HOH . 
N 5 HOH B 37 1737 33 HOH HOH . 
N 5 HOH B 38 1738 48 HOH HOH . 
N 5 HOH B 39 1739 65 HOH HOH . 
N 5 HOH B 40 1740 34 HOH HOH . 
N 5 HOH B 41 1741 55 HOH HOH . 
N 5 HOH B 42 1742 46 HOH HOH . 
N 5 HOH B 43 1743 98 HOH HOH . 
N 5 HOH B 44 1744 62 HOH HOH . 
N 5 HOH B 45 1745 99 HOH HOH . 
N 5 HOH B 46 1746 40 HOH HOH . 
N 5 HOH B 47 1747 97 HOH HOH . 
N 5 HOH B 48 1748 41 HOH HOH . 
N 5 HOH B 49 1749 63 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 CAW 5BW . . . L 4 -10.502 -5.176 44.286 1 38.92 ? CAW 5BW 1605 B 1 
HETATM 2 C CAV 5BW . . . L 4 -10.564 -5.097 42.898 1 39.89 ? CAV 5BW 1605 B 1 
HETATM 3 C CAU 5BW . . . L 4 -9.417 -5.194 42.119 1 39.64 ? CAU 5BW 1605 B 1 
HETATM 4 C CAT 5BW . . . L 4 -8.199 -5.391 42.755 1 43.59 ? CAT 5BW 1605 B 1 
HETATM 5 N NAS 5BW . . . L 4 -8.148 -5.489 44.174 1 40.22 ? NAS 5BW 1605 B 1 
HETATM 6 C CAR 5BW . . . L 4 -9.272 -5.377 44.909 1 35.42 ? CAR 5BW 1605 B 1 
HETATM 7 N NAO 5BW . . . L 4 -9.175 -5.438 46.224 1 32.95 ? NAO 5BW 1605 B 1 
HETATM 8 C CAN 5BW . . . L 4 -10.142 -4.976 47.229 1 33.49 ? CAN 5BW 1605 B 1 
HETATM 9 C CAM 5BW . . . L 4 -9.191 -4.857 48.438 1 33.15 ? CAM 5BW 1605 B 1 
HETATM 10 C CAX 5BW . . . L 4 -8.431 -6.127 48.415 1 33.73 ? CAX 5BW 1605 B 1 
HETATM 11 C CAP 5BW . . . L 4 -7.906 -5.8 47.03 1 33.5 ? CAP 5BW 1605 B 1 
HETATM 12 C CAQ 5BW . . . L 4 -7.125 -4.568 47.351 1 33.13 ? CAQ 5BW 1605 B 1 
HETATM 13 N NAL 5BW . . . L 4 -8.217 -3.824 48.023 1 32.39 ? NAL 5BW 1605 B 1 
HETATM 14 C CAK 5BW . . . L 4 -8.019 -2.882 48.956 1 31.78 ? CAK 5BW 1605 B 1 
HETATM 15 C CAH 5BW . . . L 4 -6.91 -1.89 48.803 1 26.41 ? CAH 5BW 1605 B 1 
HETATM 16 C CAG 5BW . . . L 4 -6.812 -0.712 49.729 1 25.09 ? CAG 5BW 1605 B 1 
HETATM 17 O OAI 5BW . . . L 4 -7.691 -0.479 50.571 1 25.41 ? OAI 5BW 1605 B 1 
HETATM 18 C CAE 5BW . . . L 4 -5.682 0.142 49.579 1 23.16 ? CAE 5BW 1605 B 1 
HETATM 19 C CAF 5BW . . . L 4 -4.626 -0.105 48.689 1 22.68 ? CAF 5BW 1605 B 1 
HETATM 20 C CAA 5BW . . . L 4 -3.545 0.785 48.621 1 22.62 ? CAA 5BW 1605 B 1 
HETATM 21 C CAB 5BW . . . L 4 -3.518 1.933 49.418 1 20.87 ? CAB 5BW 1605 B 1 
HETATM 22 C CAC 5BW . . . L 4 -4.554 2.174 50.331 1 22.27 ? CAC 5BW 1605 B 1 
HETATM 23 C CAD 5BW . . . L 4 -5.62 1.293 50.353 1 21.88 ? CAD 5BW 1605 B 1 
HETATM 24 O OAJ 5BW . . . L 4 -6.647 1.514 51.168 1 23.24 ? OAJ 5BW 1605 B 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           24 
#