data_3JX4
#
_model_server_result.job_id            aA9IMrZLbg-yf-WVTT01aw 
_model_server_result.datetime_utc      '2024-11-18 09:41:39' 
_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          3jx4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":800}' 
#
_entry.id    3JX4 
#
_exptl.entry_id    3JX4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              371.495 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine" 
_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            3JX4 
_cell.length_a            51.602 
_cell.length_b            110.975 
_cell.length_c            164.866 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JX4 
_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               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 
_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
? 4 E N N 
? 4 J 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 30 A CYS 326 1_555 G ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc2 A SG CYS 35 A CYS 331 1_555 G ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc3 A SG CYS 119 A CYS 415 1_555 C FE HEM . A HEM 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc4 G ZN ZN . A ZN 900 1_555 B SG CYS 30 B CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc5 G ZN ZN . A ZN 900 1_555 B SG CYS 35 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc6 B SG CYS 119 B CYS 415 1_555 H FE HEM . B HEM 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
#
_chem_comp.formula           'C21 H30 F N5' 
_chem_comp.formula_weight    371.495 
_chem_comp.id                J11 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "N-{(3R,4S)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     
;N1-{(3'R,4'S)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-fluorophenethyl)ethane-1,2-diamine tetrahydrochloride
;
#
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 N1 J11 sing 294 n n 
C1 C2 J11 sing 295 n n 
N1 C3' J11 sing 296 n n 
C2 N2 J11 sing 297 n n 
N2 C3 J11 sing 298 n n 
C3 C4 J11 sing 299 n n 
C4 C11 J11 sing 300 n n 
N1' C2' J11 sing 301 n n 
N1' C5' J11 sing 302 n n 
C11 C12 J11 doub 303 n y 
C11 C16 J11 sing 304 n y 
N11 C21 J11 doub 305 n y 
N11 C61 J11 sing 306 n y 
C12 C13 J11 sing 307 n y 
C13 F13 J11 sing 308 n n 
C13 C14 J11 doub 309 n y 
C14 C15 J11 sing 310 n y 
C15 C16 J11 doub 311 n y 
C2' C3' J11 sing 312 n n 
C21 C31 J11 sing 313 n y 
C21 C71 J11 sing 314 n n 
C3' C4' J11 sing 315 n n 
C31 C41 J11 doub 316 n y 
C4' C5' J11 sing 317 n n 
C4' C71 J11 sing 318 n n 
C41 C51 J11 sing 319 n y 
C41 C81 J11 sing 320 n n 
C51 C61 J11 doub 321 n y 
C61 N61 J11 sing 322 n n 
C1 H1 J11 sing 323 n n 
C1 H1A J11 sing 324 n n 
N1 HN1 J11 sing 325 n n 
C2 H2 J11 sing 326 n n 
C2 H2A J11 sing 327 n n 
N2 HN2 J11 sing 328 n n 
C3 H3 J11 sing 329 n n 
C3 H3A J11 sing 330 n n 
C4 H4 J11 sing 331 n n 
C4 H4A J11 sing 332 n n 
N1' HN1' J11 sing 333 n n 
C12 H12 J11 sing 334 n n 
C14 H14 J11 sing 335 n n 
C15 H15 J11 sing 336 n n 
C16 H16 J11 sing 337 n n 
C2' H2' J11 sing 338 n n 
C2' "H2'A" J11 sing 339 n n 
C3' H3' J11 sing 340 n n 
C31 H31 J11 sing 341 n n 
C4' H4' J11 sing 342 n n 
C5' H5' J11 sing 343 n n 
C5' "H5'A" J11 sing 344 n n 
C51 H51 J11 sing 345 n n 
N61 HN61 J11 sing 346 n n 
N61 HN6A J11 sing 347 n n 
C71 H71 J11 sing 348 n n 
C71 H71A J11 sing 349 n n 
C81 H81 J11 sing 350 n n 
C81 H81A J11 sing 351 n n 
C81 H81B J11 sing 352 n n 
#
_atom_sites.entry_id                     3JX4 
_atom_sites.fract_transf_matrix[1][1]    0.019379 
_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]    0.009011 
_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]    0.006066 
_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 1 750 750 HEM HEM . 
D 3 H4B A 1 760 760 H4B H4B . 
E 4 J11 A 1 800 800 J11 J11 . 
F 5 ACT A 1 860 860 ACT ACT . 
G 6 ZN A 1 900 900 ZN ZN . 
H 2 HEM B 1 750 750 HEM HEM . 
I 3 H4B B 1 760 760 H4B H4B . 
J 4 J11 B 1 800 800 J11 J11 . 
K 5 ACT B 1 860 860 ACT ACT . 
L 7 HOH A 1 1000 1000 HOH HOH . 
L 7 HOH A 2 1001 1001 HOH HOH . 
L 7 HOH A 3 1002 1002 HOH HOH . 
L 7 HOH A 4 1003 1003 HOH HOH . 
L 7 HOH A 5 1004 1004 HOH HOH . 
L 7 HOH A 6 1005 1005 HOH HOH . 
L 7 HOH A 7 1006 1006 HOH HOH . 
L 7 HOH A 8 1007 1007 HOH HOH . 
L 7 HOH A 9 1008 1008 HOH HOH . 
L 7 HOH A 10 1009 1009 HOH HOH . 
L 7 HOH A 11 1010 1010 HOH HOH . 
L 7 HOH A 12 1011 1011 HOH HOH . 
L 7 HOH A 13 1012 1012 HOH HOH . 
L 7 HOH A 14 1013 1013 HOH HOH . 
L 7 HOH A 15 1014 1014 HOH HOH . 
L 7 HOH A 16 1015 1015 HOH HOH . 
L 7 HOH A 17 1016 1016 HOH HOH . 
L 7 HOH A 18 1017 1017 HOH HOH . 
L 7 HOH A 19 1018 1018 HOH HOH . 
L 7 HOH A 20 1019 1019 HOH HOH . 
L 7 HOH A 21 1020 1020 HOH HOH . 
L 7 HOH A 22 1021 1021 HOH HOH . 
L 7 HOH A 23 1022 1022 HOH HOH . 
L 7 HOH A 24 1023 1023 HOH HOH . 
L 7 HOH A 25 1024 1024 HOH HOH . 
L 7 HOH A 26 1025 1025 HOH HOH . 
L 7 HOH A 27 1026 1026 HOH HOH . 
L 7 HOH A 28 1027 1027 HOH HOH . 
L 7 HOH A 29 1028 1028 HOH HOH . 
L 7 HOH A 30 1029 1029 HOH HOH . 
L 7 HOH A 31 1030 1030 HOH HOH . 
L 7 HOH A 32 1031 1031 HOH HOH . 
L 7 HOH A 33 1032 1032 HOH HOH . 
L 7 HOH A 34 1033 1033 HOH HOH . 
L 7 HOH A 35 1034 1034 HOH HOH . 
L 7 HOH A 36 1035 1035 HOH HOH . 
L 7 HOH A 37 1036 1036 HOH HOH . 
L 7 HOH A 38 1037 1037 HOH HOH . 
L 7 HOH A 39 1038 1038 HOH HOH . 
L 7 HOH A 40 1039 1039 HOH HOH . 
L 7 HOH A 41 1040 1040 HOH HOH . 
L 7 HOH A 42 1041 1041 HOH HOH . 
L 7 HOH A 43 1042 1042 HOH HOH . 
L 7 HOH A 44 1043 1043 HOH HOH . 
L 7 HOH A 45 1044 1044 HOH HOH . 
L 7 HOH A 46 1045 1045 HOH HOH . 
L 7 HOH A 47 1046 1046 HOH HOH . 
L 7 HOH A 48 1047 1047 HOH HOH . 
L 7 HOH A 49 1048 1048 HOH HOH . 
L 7 HOH A 50 1049 1049 HOH HOH . 
L 7 HOH A 51 1050 1050 HOH HOH . 
L 7 HOH A 52 1051 1051 HOH HOH . 
M 7 HOH B 1 1000 1000 HOH HOH . 
M 7 HOH B 2 1001 1001 HOH HOH . 
M 7 HOH B 3 1002 1002 HOH HOH . 
M 7 HOH B 4 1003 1003 HOH HOH . 
M 7 HOH B 5 1004 1004 HOH HOH . 
M 7 HOH B 6 1005 1005 HOH HOH . 
M 7 HOH B 7 1006 1006 HOH HOH . 
M 7 HOH B 8 1007 1007 HOH HOH . 
M 7 HOH B 9 1008 1008 HOH HOH . 
M 7 HOH B 10 1009 1009 HOH HOH . 
M 7 HOH B 11 1010 1010 HOH HOH . 
M 7 HOH B 12 1011 1011 HOH HOH . 
M 7 HOH B 13 1012 1012 HOH HOH . 
M 7 HOH B 14 1013 1013 HOH HOH . 
M 7 HOH B 15 1014 1014 HOH HOH . 
M 7 HOH B 16 1015 1015 HOH HOH . 
M 7 HOH B 17 1016 1016 HOH HOH . 
M 7 HOH B 18 1017 1017 HOH HOH . 
M 7 HOH B 19 1018 1018 HOH HOH . 
M 7 HOH B 20 1019 1019 HOH HOH . 
M 7 HOH B 21 1020 1020 HOH HOH . 
M 7 HOH B 22 1021 1021 HOH HOH . 
M 7 HOH B 23 1022 1022 HOH HOH . 
M 7 HOH B 24 1023 1023 HOH HOH . 
M 7 HOH B 25 1024 1024 HOH HOH . 
M 7 HOH B 26 1025 1025 HOH HOH . 
M 7 HOH B 27 1026 1026 HOH HOH . 
M 7 HOH B 28 1027 1027 HOH HOH . 
M 7 HOH B 29 1028 1028 HOH HOH . 
M 7 HOH B 30 1029 1029 HOH HOH . 
M 7 HOH B 31 1030 1030 HOH HOH . 
M 7 HOH B 32 1031 1031 HOH HOH . 
M 7 HOH B 33 1032 1032 HOH HOH . 
M 7 HOH B 34 1033 1033 HOH HOH . 
M 7 HOH B 35 1034 1034 HOH HOH . 
M 7 HOH B 36 1035 1035 HOH HOH . 
M 7 HOH B 37 1036 1036 HOH HOH . 
M 7 HOH B 38 1037 1037 HOH HOH . 
M 7 HOH B 39 1038 1038 HOH HOH . 
M 7 HOH B 40 1039 1039 HOH HOH . 
M 7 HOH B 41 1040 1040 HOH HOH . 
M 7 HOH B 42 1041 1041 HOH HOH . 
M 7 HOH B 43 1042 1042 HOH HOH . 
M 7 HOH B 44 1043 1043 HOH HOH . 
M 7 HOH B 45 1044 1044 HOH HOH . 
M 7 HOH B 46 1045 1045 HOH HOH . 
M 7 HOH B 47 1046 1046 HOH HOH . 
M 7 HOH B 48 1047 1047 HOH HOH . 
M 7 HOH B 49 1048 1048 HOH HOH . 
M 7 HOH B 50 1049 1049 HOH HOH . 
M 7 HOH B 51 1050 1050 HOH HOH . 
M 7 HOH B 52 1051 1051 HOH HOH . 
M 7 HOH B 53 1052 1052 HOH HOH . 
M 7 HOH B 54 1053 1053 HOH HOH . 
M 7 HOH B 55 1054 1054 HOH HOH . 
M 7 HOH B 56 1055 1055 HOH HOH . 
M 7 HOH B 57 1056 1056 HOH HOH . 
M 7 HOH B 58 1057 1057 HOH HOH . 
M 7 HOH B 59 1058 1058 HOH HOH . 
M 7 HOH B 60 1059 1059 HOH HOH . 
M 7 HOH B 61 1060 1060 HOH HOH . 
M 7 HOH B 62 1061 1061 HOH HOH . 
M 7 HOH B 63 1062 1062 HOH HOH . 
M 7 HOH B 64 1063 1063 HOH HOH . 
M 7 HOH B 65 1064 1064 HOH HOH . 
M 7 HOH B 66 1065 1065 HOH HOH . 
M 7 HOH B 67 1066 1066 HOH HOH . 
M 7 HOH B 68 1067 1067 HOH HOH . 
M 7 HOH B 69 1068 1068 HOH HOH . 
M 7 HOH B 70 1069 1069 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 J11 . . . J 4 16.281 4.469 58.314 1 60.99 ? C1 J11 800 B 1 
HETATM 2 N N1 J11 . . . J 4 16.736 3.462 57.373 1 58.94 ? N1 J11 800 B 1 
HETATM 3 C C2 J11 . . . J 4 16.279 5.889 57.771 1 66.06 ? C2 J11 800 B 1 
HETATM 4 N N2 J11 . . . J 4 17.599 6.378 57.364 1 70.01 ? N2 J11 800 B 1 
HETATM 5 C C3 J11 . . . J 4 18.083 6.254 55.995 1 71.94 ? C3 J11 800 B 1 
HETATM 6 C C4 J11 . . . J 4 17.757 7.425 55.06 1 74.29 ? C4 J11 800 B 1 
HETATM 7 N N1' J11 . . . J 4 16.122 -0.088 57.02 1 53.54 ? N1' J11 800 B 1 
HETATM 8 C C11 J11 . . . J 4 18.922 8.332 54.712 1 75.89 ? C11 J11 800 B 1 
HETATM 9 N N11 J11 . . . J 4 12.259 0.002 58.441 1 52.16 ? N11 J11 800 B 1 
HETATM 10 C C12 J11 . . . J 4 18.718 9.713 54.711 1 77.28 ? C12 J11 800 B 1 
HETATM 11 C C13 J11 . . . J 4 19.774 10.581 54.408 1 81.19 ? C13 J11 800 B 1 
HETATM 12 F F13 J11 . . . J 4 19.578 11.921 54.407 1 83.94 ? F13 J11 800 B 1 
HETATM 13 C C14 J11 . . . J 4 21.035 10.062 54.098 1 81.48 ? C14 J11 800 B 1 
HETATM 14 C C15 J11 . . . J 4 21.238 8.679 54.093 1 80.73 ? C15 J11 800 B 1 
HETATM 15 C C16 J11 . . . J 4 20.183 7.814 54.399 1 77.91 ? C16 J11 800 B 1 
HETATM 16 C C2' J11 . . . J 4 16.796 1.094 56.507 1 55.86 ? C2' J11 800 B 1 
HETATM 17 C C21 J11 . . . J 4 12.644 1.248 58.805 1 52.84 ? C21 J11 800 B 1 
HETATM 18 C C3' J11 . . . J 4 15.956 2.26 57.066 1 56.73 ? C3' J11 800 B 1 
HETATM 19 C C31 J11 . . . J 4 12.046 1.851 59.93 1 53.1 ? C31 J11 800 B 1 
HETATM 20 C C4' J11 . . . J 4 15.149 1.691 58.242 1 52.91 ? C4' J11 800 B 1 
HETATM 21 C C41 J11 . . . J 4 11.082 1.159 60.679 1 55.44 ? C41 J11 800 B 1 
HETATM 22 C C5' J11 . . . J 4 15.451 0.19 58.277 1 52.99 ? C5' J11 800 B 1 
HETATM 23 C C51 J11 . . . J 4 10.705 -0.107 60.252 1 53.22 ? C51 J11 800 B 1 
HETATM 24 C C61 J11 . . . J 4 11.297 -0.669 59.124 1 52.02 ? C61 J11 800 B 1 
HETATM 25 N N61 J11 . . . J 4 10.923 -1.903 58.727 1 46.68 ? N61 J11 800 B 1 
HETATM 26 C C71 J11 . . . J 4 13.689 1.996 57.975 1 49.58 ? C71 J11 800 B 1 
HETATM 27 C C81 J11 . . . J 4 10.41 1.764 61.901 1 54.29 ? C81 J11 800 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#