data_6B3E
#
_model_server_result.job_id            8i8d_C1tX7ldJdERODPUkA 
_model_server_result.datetime_utc      '2024-11-04 20:29:46' 
_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          6b3e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1102}' 
#
_entry.id    6B3E 
#
_exptl.entry_id    6B3E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              456.492 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl)methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         76.53 
_cell.angle_beta          85.28 
_cell.angle_gamma         78.22 
_cell.entry_id            6B3E 
_cell.length_a            50.14 
_cell.length_b            77.26 
_cell.length_c            90.64 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6B3E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,E,F,G,H,L,M 1 1 
C,D,I,J,K,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 F N N 
? 4 K 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
covale ? covale1 A C TYR 176 A TYR 892 1_555 A N TPO 177 A TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
covale ? covale2 A C TPO 177 A TPO 893 1_555 A N ASN 178 A ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale3 C C TYR 176 C TYR 892 1_555 C N TPO 177 C TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale4 C C TPO 177 C TPO 893 1_555 C N ASN 178 C ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
metalc ? metalc1 A OD2 ASP 143 A ASP 859 1_555 E MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? 
metalc ? metalc2 A OD2 ASP 161 A ASP 877 1_555 E MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc3 C OD2 ASP 143 C ASP 859 1_555 I MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? 
metalc ? metalc4 C OD2 ASP 161 C ASP 877 1_555 I MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
#
_chem_comp.formula           'C22 H26 F2 N8 O' 
_chem_comp.formula_weight    456.492 
_chem_comp.id                CJM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl)methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol 
_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
C19 C20 CJM doub 70 n y 
C19 C17 CJM sing 71 n y 
N18 C17 CJM sing 72 n y 
N18 C14 CJM sing 73 n y 
N5 C4 CJM doub 74 n y 
N5 C6 CJM sing 75 n y 
C20 C21 CJM sing 76 n y 
C4 N3 CJM sing 77 n y 
C17 C16 CJM doub 78 n y 
N12 C13 CJM sing 79 n n 
N12 C11 CJM sing 80 n n 
C14 C13 CJM sing 81 n n 
C14 N15 CJM doub 82 n y 
C6 C11 CJM doub 83 n y 
C6 C7 CJM sing 84 n y 
N3 C7 CJM sing 85 n y 
N3 C2 CJM sing 86 n n 
C11 N10 CJM sing 87 n y 
C21 F24 CJM sing 88 n n 
C21 C22 CJM doub 89 n y 
C16 N15 CJM sing 90 n y 
C16 C22 CJM sing 91 n y 
C7 N8 CJM doub 92 n y 
C2 C1 CJM sing 93 n n 
C22 F23 CJM sing 94 n n 
N10 C9 CJM doub 95 n y 
N8 C9 CJM sing 96 n y 
C9 N25 CJM sing 97 n n 
N25 C26 CJM sing 98 n n 
N25 C30 CJM sing 99 n n 
C26 C27 CJM sing 100 n n 
C30 C29 CJM sing 101 n n 
C30 C31 CJM sing 102 n n 
O33 C32 CJM sing 103 n n 
C28 C27 CJM sing 104 n n 
C28 C29 CJM sing 105 n n 
C32 C31 CJM sing 106 n n 
C1 H1 CJM sing 107 n n 
C1 H2 CJM sing 108 n n 
C1 H3 CJM sing 109 n n 
C2 H4 CJM sing 110 n n 
C2 H5 CJM sing 111 n n 
C13 H6 CJM sing 112 n n 
C13 H7 CJM sing 113 n n 
N18 H8 CJM sing 114 n n 
C19 H9 CJM sing 115 n n 
C20 H10 CJM sing 116 n n 
C27 H11 CJM sing 117 n n 
C27 H12 CJM sing 118 n n 
C30 H13 CJM sing 119 n n 
C31 H14 CJM sing 120 n n 
C31 H15 CJM sing 121 n n 
C32 H16 CJM sing 122 n n 
C32 H17 CJM sing 123 n n 
C4 H18 CJM sing 124 n n 
N12 H19 CJM sing 125 n n 
C26 H21 CJM sing 126 n n 
C26 H22 CJM sing 127 n n 
C28 H23 CJM sing 128 n n 
C28 H24 CJM sing 129 n n 
C29 H25 CJM sing 130 n n 
C29 H26 CJM sing 131 n n 
O33 H27 CJM sing 132 n n 
#
_atom_sites.entry_id                     6B3E 
_atom_sites.fract_transf_matrix[1][1]    0.019944 
_atom_sites.fract_transf_matrix[1][2]    -0.004159 
_atom_sites.fract_transf_matrix[1][3]    -0.000744 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013222 
_atom_sites.fract_transf_matrix[2][3]    -0.003004 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011352 
_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
E 3 MG A 1 1101 2 MG MG . 
F 4 CJM A 1 1102 1 CJM INH . 
G 5 EDO B 1 301 2 EDO EDO . 
H 5 EDO B 1 302 3 EDO EDO . 
I 3 MG C 1 1101 1 MG MG . 
J 5 EDO C 1 1102 1 EDO EDO . 
K 4 CJM C 1 1103 2 CJM INH . 
L 6 HOH A 1 1201 4 HOH HOH . 
L 6 HOH A 2 1202 3 HOH HOH . 
L 6 HOH A 3 1203 5 HOH HOH . 
L 6 HOH A 4 1204 6 HOH HOH . 
L 6 HOH A 5 1205 2 HOH HOH . 
L 6 HOH A 6 1206 7 HOH HOH . 
M 6 HOH B 1 401 9 HOH HOH . 
N 6 HOH D 1 301 1 HOH HOH . 
N 6 HOH D 2 302 8 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 CJM . . . F 4 -0.033 14.517 -6.849 1 61.43 ? C1 CJM 1102 A 1 
HETATM 2 C C2 CJM . . . F 4 0.891 15.161 -7.803 1 58.23 ? C2 CJM 1102 A 1 
HETATM 3 C C7 CJM . . . F 4 0.315 17.603 -7.823 1 61.25 ? C7 CJM 1102 A 1 
HETATM 4 C C9 CJM . . . F 4 0.735 19.268 -6.42 1 59.02 ? C9 CJM 1102 A 1 
HETATM 5 C C11 CJM . . . F 4 -0.409 19.778 -8.356 1 58 ? C11 CJM 1102 A 1 
HETATM 6 C C13 CJM . . . F 4 -1.358 21.998 -8.627 1 59.07 ? C13 CJM 1102 A 1 
HETATM 7 C C14 CJM . . . F 4 -0.205 22.882 -8.781 1 63.76 ? C14 CJM 1102 A 1 
HETATM 8 C C16 CJM . . . F 4 1.405 24.217 -8.17 1 63.31 ? C16 CJM 1102 A 1 
HETATM 9 N N18 CJM . . . F 4 0.451 23.136 -9.893 1 70.7 ? N18 CJM 1102 A 1 
HETATM 10 C C19 CJM . . . F 4 2.494 24.577 -10.266 1 62.34 ? C19 CJM 1102 A 1 
HETATM 11 C C20 CJM . . . F 4 3.428 25.393 -9.66 1 60.43 ? C20 CJM 1102 A 1 
HETATM 12 C C21 CJM . . . F 4 3.343 25.599 -8.312 1 65.37 ? C21 CJM 1102 A 1 
HETATM 13 C C22 CJM . . . F 4 2.348 25.028 -7.568 1 65.44 ? C22 CJM 1102 A 1 
HETATM 14 N N25 CJM . . . F 4 1.344 19.757 -5.271 1 56.78 ? N25 CJM 1102 A 1 
HETATM 15 C C27 CJM . . . F 4 1.923 21.549 -3.655 1 56.73 ? C27 CJM 1102 A 1 
HETATM 16 C C30 CJM . . . F 4 1.856 18.786 -4.292 1 56.64 ? C30 CJM 1102 A 1 
HETATM 17 C C31 CJM . . . F 4 0.761 18.36 -3.325 1 57.63 ? C31 CJM 1102 A 1 
HETATM 18 C C32 CJM . . . F 4 0.198 16.997 -3.633 1 59.12 ? C32 CJM 1102 A 1 
HETATM 19 N N3 CJM . . . F 4 0.315 16.358 -8.391 1 59.13 ? N3 CJM 1102 A 1 
HETATM 20 C C4 CJM . . . F 4 -0.301 16.505 -9.593 1 61.29 ? C4 CJM 1102 A 1 
HETATM 21 N N5 CJM . . . F 4 -0.701 17.725 -9.844 1 63.84 ? N5 CJM 1102 A 1 
HETATM 22 C C6 CJM . . . F 4 -0.312 18.431 -8.719 1 60.7 ? C6 CJM 1102 A 1 
HETATM 23 N N8 CJM . . . F 4 0.849 17.953 -6.661 1 61.51 ? N8 CJM 1102 A 1 
HETATM 24 N N10 CJM . . . F 4 0.128 20.175 -7.201 1 58.05 ? N10 CJM 1102 A 1 
HETATM 25 N N12 CJM . . . F 4 -1.048 20.68 -9.102 1 58.56 ? N12 CJM 1102 A 1 
HETATM 26 N N15 CJM . . . F 4 0.325 23.514 -7.717 1 60.42 ? N15 CJM 1102 A 1 
HETATM 27 C C17 CJM . . . F 4 1.482 23.987 -9.509 1 67.46 ? C17 CJM 1102 A 1 
HETATM 28 F F23 CJM . . . F 4 2.295 25.243 -6.246 1 69.43 ? F23 CJM 1102 A 1 
HETATM 29 F F24 CJM . . . F 4 4.271 26.339 -7.688 1 71.05 ? F24 CJM 1102 A 1 
HETATM 30 C C26 CJM . . . F 4 1.001 21.084 -4.757 1 55.16 ? C26 CJM 1102 A 1 
HETATM 31 C C28 CJM . . . F 4 3.256 20.845 -3.719 1 56.14 ? C28 CJM 1102 A 1 
HETATM 32 C C29 CJM . . . F 4 3.096 19.334 -3.591 1 53.98 ? C29 CJM 1102 A 1 
HETATM 33 O O33 CJM . . . F 4 1.218 16.105 -3.983 1 58.93 ? O33 CJM 1102 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#