data_3NLT
#
_model_server_result.job_id            BsG4PREsPp3nywOmRDho1g 
_model_server_result.datetime_utc      '2025-01-25 10:48:41' 
_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          3nlt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":800}' 
#
_entry.id    3NLT 
#
_exptl.entry_id    3NLT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              397.506 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-({(3S,4S)-4-[2-({2,2-difluoro-2-[(2R)-piperidin-2-yl]ethyl}amino)ethoxy]pyrrolidin-3-yl}methyl)-4-methylpyridin-2-amine 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3NLT 
_cell.length_a            57.91 
_cell.length_b            106.905 
_cell.length_c            157.024 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NLT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 F N N 
? 5 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 SG CYS 58 A CYS 96 1_555 H ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc2 A SG CYS 63 A CYS 101 1_555 H ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc3 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc4 H ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc5 H ZN ZN . A ZN 900 1_555 B SG CYS 63 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc6 B SG CYS 148 B CYS 186 1_555 I FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
#
_chem_comp.formula           'C20 H33 F2 N5 O' 
_chem_comp.formula_weight    397.506 
_chem_comp.id                3XF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-({(3S,4S)-4-[2-({2,2-difluoro-2-[(2R)-piperidin-2-yl]ethyl}amino)ethoxy]pyrrolidin-3-yl}methyl)-4-methylpyridin-2-amine 
_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
O1 C3' 3XF sing 1 n n 
O1 C2 3XF sing 2 n n 
C3 C2 3XF sing 3 n n 
C2 H2 3XF sing 4 n n 
C2 H2A 3XF sing 5 n n 
N4 C3 3XF sing 6 n n 
C3 H3 3XF sing 7 n n 
C3 H3A 3XF sing 8 n n 
C5 N4 3XF sing 9 n n 
N4 HN4 3XF sing 10 n n 
C6 C5 3XF sing 11 n n 
C5 H5 3XF sing 12 n n 
C5 H5A 3XF sing 13 n n 
F7 C6 3XF sing 14 n n 
F8 C6 3XF sing 15 n n 
C6 C12 3XF sing 16 n n 
C2' N1' 3XF sing 17 n n 
N1' C5' 3XF sing 18 n n 
N1' HN1' 3XF sing 19 n n 
C12 N11 3XF sing 20 n n 
N11 C16 3XF sing 21 n n 
N11 HN11 3XF sing 22 n n 
C13 C12 3XF sing 23 n n 
C12 H12 3XF sing 24 n n 
C13 C14 3XF sing 25 n n 
C13 H13 3XF sing 26 n n 
C13 H13A 3XF sing 27 n n 
C14 C15 3XF sing 28 n n 
C14 H14 3XF sing 29 n n 
C14 H14A 3XF sing 30 n n 
C15 C16 3XF sing 31 n n 
C15 H15 3XF sing 32 n n 
C15 H15A 3XF sing 33 n n 
C16 H16 3XF sing 34 n n 
C16 H16A 3XF sing 35 n n 
N1A C2A 3XF doub 36 n y 
N1A C6A 3XF sing 37 n y 
C2' C3' 3XF sing 38 n n 
C2' H2' 3XF sing 39 n n 
C2' "H2'A" 3XF sing 40 n n 
C7A C2A 3XF sing 41 n n 
C2A C3A 3XF sing 42 n y 
C3' C4' 3XF sing 43 n n 
C3' H3' 3XF sing 44 n n 
C3A C4A 3XF doub 45 n y 
C3A H3AA 3XF sing 46 n n 
C5' C4' 3XF sing 47 n n 
C7A C4' 3XF sing 48 n n 
C4' H4' 3XF sing 49 n n 
C5A C4A 3XF sing 50 n y 
C4A C8A 3XF sing 51 n n 
C5' H5' 3XF sing 52 n n 
C5' "H5'A" 3XF sing 53 n n 
C6A C5A 3XF doub 54 n y 
C5A H5AA 3XF sing 55 n n 
N6A C6A 3XF sing 56 n n 
N6A HN6A 3XF sing 57 n n 
N6A HN6B 3XF sing 58 n n 
C7A H7A 3XF sing 59 n n 
C7A H7AA 3XF sing 60 n n 
C8A H8A 3XF sing 61 n n 
C8A H8AA 3XF sing 62 n n 
C8A H8AB 3XF sing 63 n n 
#
_atom_sites.entry_id                     3NLT 
_atom_sites.fract_transf_matrix[1][1]    0.017268 
_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]    0.009354 
_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]    0.006368 
_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 HEM A 1 500 500 HEM HEM . 
D 3 H4B A 1 600 600 H4B H4B . 
E 4 GOL A 1 880 880 GOL GOL . 
F 5 3XF A 1 800 800 3XF 3XF . 
G 6 CAD A 1 950 950 CAD CAD . 
H 7 ZN A 1 900 900 ZN ZN . 
I 2 HEM B 1 500 500 HEM HEM . 
J 3 H4B B 1 600 600 H4B H4B . 
K 4 GOL B 1 880 880 GOL GOL . 
L 5 3XF B 1 800 800 3XF 3XF . 
M 6 CAD B 1 950 950 CAD CAD . 
N 8 HOH A 1 1001 1001 HOH HOH . 
N 8 HOH A 2 1002 1002 HOH HOH . 
N 8 HOH A 3 1003 1003 HOH HOH . 
N 8 HOH A 4 1004 1004 HOH HOH . 
N 8 HOH A 5 1005 1005 HOH HOH . 
N 8 HOH A 6 1006 1006 HOH HOH . 
N 8 HOH A 7 1007 1007 HOH HOH . 
N 8 HOH A 8 1008 1008 HOH HOH . 
N 8 HOH A 9 1009 1009 HOH HOH . 
N 8 HOH A 10 1010 1010 HOH HOH . 
N 8 HOH A 11 1011 1011 HOH HOH . 
N 8 HOH A 12 1012 1012 HOH HOH . 
N 8 HOH A 13 1013 1013 HOH HOH . 
N 8 HOH A 14 1014 1014 HOH HOH . 
N 8 HOH A 15 1015 1015 HOH HOH . 
N 8 HOH A 16 1016 1016 HOH HOH . 
N 8 HOH A 17 1017 1017 HOH HOH . 
N 8 HOH A 18 1018 1018 HOH HOH . 
N 8 HOH A 19 1019 1019 HOH HOH . 
N 8 HOH A 20 1020 1020 HOH HOH . 
N 8 HOH A 21 1021 1021 HOH HOH . 
N 8 HOH A 22 1022 1022 HOH HOH . 
N 8 HOH A 23 1023 1023 HOH HOH . 
N 8 HOH A 24 1024 1024 HOH HOH . 
N 8 HOH A 25 1025 1025 HOH HOH . 
N 8 HOH A 26 1026 1026 HOH HOH . 
N 8 HOH A 27 1027 1027 HOH HOH . 
N 8 HOH A 28 1028 1028 HOH HOH . 
N 8 HOH A 29 1029 1029 HOH HOH . 
N 8 HOH A 30 1030 1030 HOH HOH . 
N 8 HOH A 31 1031 1031 HOH HOH . 
N 8 HOH A 32 1032 1032 HOH HOH . 
O 8 HOH B 1 1001 1001 HOH HOH . 
O 8 HOH B 2 1002 1002 HOH HOH . 
O 8 HOH B 3 1003 1003 HOH HOH . 
O 8 HOH B 4 1004 1004 HOH HOH . 
O 8 HOH B 5 1005 1005 HOH HOH . 
O 8 HOH B 6 1006 1006 HOH HOH . 
O 8 HOH B 7 1007 1007 HOH HOH . 
O 8 HOH B 8 1008 1008 HOH HOH . 
O 8 HOH B 9 1009 1009 HOH HOH . 
O 8 HOH B 10 1010 1010 HOH HOH . 
O 8 HOH B 11 1011 1011 HOH HOH . 
O 8 HOH B 12 1012 1012 HOH HOH . 
O 8 HOH B 13 1013 1013 HOH HOH . 
O 8 HOH B 14 1014 1014 HOH HOH . 
O 8 HOH B 15 1015 1015 HOH HOH . 
O 8 HOH B 16 1016 1016 HOH HOH . 
O 8 HOH B 17 1017 1017 HOH HOH . 
O 8 HOH B 18 1018 1018 HOH HOH . 
O 8 HOH B 19 1019 1019 HOH HOH . 
O 8 HOH B 20 1020 1020 HOH HOH . 
O 8 HOH B 21 1021 1021 HOH HOH . 
O 8 HOH B 22 1022 1022 HOH HOH . 
O 8 HOH B 23 1023 1023 HOH HOH . 
O 8 HOH B 24 1024 1024 HOH HOH . 
O 8 HOH B 25 1025 1025 HOH HOH . 
O 8 HOH B 26 1026 1026 HOH HOH . 
O 8 HOH B 27 1027 1027 HOH HOH . 
O 8 HOH B 28 1028 1028 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 O O1 3XF . . . F 5 11.042 14.103 34.705 1 48.35 ? O1 3XF 800 A 1 
HETATM 2 C C2 3XF . . . F 5 12.417 14.334 34.373 1 54.88 ? C2 3XF 800 A 1 
HETATM 3 C C3 3XF . . . F 5 13.384 13.758 35.424 1 61.61 ? C3 3XF 800 A 1 
HETATM 4 N N4 3XF . . . F 5 13.123 14.217 36.792 1 68.34 ? N4 3XF 800 A 1 
HETATM 5 C C5 3XF . . . F 5 14.179 14.492 37.777 1 73.24 ? C5 3XF 800 A 1 
HETATM 6 C C6 3XF . . . F 5 14.528 15.983 37.939 1 76.77 ? C6 3XF 800 A 1 
HETATM 7 F F7 3XF . . . F 5 13.651 16.748 37.27 1 76.81 ? F7 3XF 800 A 1 
HETATM 8 F F8 3XF . . . F 5 14.498 16.309 39.242 1 76.55 ? F8 3XF 800 A 1 
HETATM 9 N N1' 3XF . . . F 5 7.957 16.025 34.368 1 44.04 ? N1' 3XF 800 A 1 
HETATM 10 N N11 3XF . . . F 5 16.174 15.888 36.001 1 76.39 ? N11 3XF 800 A 1 
HETATM 11 C C12 3XF . . . F 5 15.941 16.315 37.389 1 77.23 ? C12 3XF 800 A 1 
HETATM 12 C C13 3XF . . . F 5 17.115 16.05 38.354 1 77.11 ? C13 3XF 800 A 1 
HETATM 13 C C14 3XF . . . F 5 17.791 14.711 38.057 1 76.91 ? C14 3XF 800 A 1 
HETATM 14 C C15 3XF . . . F 5 18.206 14.597 36.585 1 77.39 ? C15 3XF 800 A 1 
HETATM 15 C C16 3XF . . . F 5 17.006 14.744 35.65 1 77.17 ? C16 3XF 800 A 1 
HETATM 16 N N1A 3XF . . . F 5 6.815 12.252 32.479 1 36.95 ? N1A 3XF 800 A 1 
HETATM 17 C C2' 3XF . . . F 5 9.163 15.755 35.139 1 46.52 ? C2' 3XF 800 A 1 
HETATM 18 C C2A 3XF . . . F 5 8.152 12.258 32.315 1 35.87 ? C2A 3XF 800 A 1 
HETATM 19 C C3' 3XF . . . F 5 10.135 15.072 34.134 1 46.29 ? C3' 3XF 800 A 1 
HETATM 20 C C3A 3XF . . . F 5 8.727 11.545 31.257 1 33.65 ? C3A 3XF 800 A 1 
HETATM 21 C C4' 3XF . . . F 5 9.231 14.493 33.04 1 43.22 ? C4' 3XF 800 A 1 
HETATM 22 C C4A 3XF . . . F 5 7.894 10.848 30.375 1 32.26 ? C4A 3XF 800 A 1 
HETATM 23 C C5' 3XF . . . F 5 7.981 15.39 33.052 1 43.75 ? C5' 3XF 800 A 1 
HETATM 24 C C5A 3XF . . . F 5 6.512 10.861 30.561 1 34.27 ? C5A 3XF 800 A 1 
HETATM 25 C C6A 3XF . . . F 5 5.983 11.588 31.639 1 37.98 ? C6A 3XF 800 A 1 
HETATM 26 N N6A 3XF . . . F 5 4.636 11.656 31.88 1 39.95 ? N6A 3XF 800 A 1 
HETATM 27 C C7A 3XF . . . F 5 8.969 13.018 33.329 1 37.6 ? C7A 3XF 800 A 1 
HETATM 28 C C8A 3XF . . . F 5 8.479 10.093 29.225 1 27.77 ? C8A 3XF 800 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#