data_5F4R
#
_model_server_result.job_id            yDCp397y6micNfXWyA0awQ 
_model_server_result.datetime_utc      '2024-10-18 00:26:50' 
_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          5f4r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":508}' 
#
_entry.id    5F4R 
#
_exptl.entry_id    5F4R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              488.946 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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            5F4R 
_cell.length_a            67.679 
_cell.length_b            127.357 
_cell.length_c            192.064 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5F4R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 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,P,Q,R,S,T 
_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 J N N 
? 4 R 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
disulf ? disulf1 A SG CYS 6 A CYS 54 1_555 A SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 71 A CYS 119 1_555 A SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf3 A SG CYS 97 A CYS 218 1_555 A SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf4 A SG CYS 107 A CYS 228 1_555 A SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 A SG CYS 175 A CYS 296 1_555 A SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 A SG CYS 240 A CYS 378 1_555 A SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 A SG CYS 247 A CYS 385 1_555 A SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 B SG CYS 6 C CYS 54 1_555 B SG CYS 26 C CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf9 B SG CYS 97 C CYS 218 1_555 B SG CYS 126 C CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf10 B SG CYS 107 C CYS 228 1_555 B SG CYS 118 C CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf11 B SG CYS 175 C CYS 296 1_555 B SG CYS 194 C CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf12 B SG CYS 240 C CYS 378 1_555 B SG CYS 304 C CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf13 B SG CYS 247 C CYS 385 1_555 B SG CYS 277 C CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
#
_chem_comp.formula           'C22 H26 Cl F N8 O2' 
_chem_comp.formula_weight    488.946 
_chem_comp.id                5VF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" 
_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
NBD CBB 5VF doub 1 n n 
CAF CAG 5VF doub 2 n y 
CAF CAD 5VF sing 3 n y 
NBA CBB 5VF sing 4 n n 
NBA CAZ 5VF sing 5 n n 
CBB NBC 5VF sing 6 n n 
CAG CAH 5VF sing 7 n y 
CLAE CAD 5VF sing 8 n n 
CAD CAB 5VF doub 9 n y 
CAZ CAY 5VF sing 10 n n 
CAH NAI 5VF sing 11 n n 
CAH CAA 5VF doub 12 n y 
CAY CAX 5VF sing 13 n n 
CAY CAO 5VF sing 14 n n 
NAI CAJ 5VF sing 15 n n 
CAX CAW 5VF sing 16 n n 
CAB CAA 5VF sing 17 n y 
CAB FAC 5VF sing 18 n n 
OAM CAL 5VF doub 19 n n 
CAJ CAL 5VF sing 20 n n 
CAJ OAK 5VF doub 21 n n 
CAL NAN 5VF sing 22 n n 
NAN CAO 5VF sing 23 n n 
CAO CAP 5VF sing 24 n n 
CAW CAP 5VF doub 25 n y 
CAW CAV 5VF sing 26 n y 
CAP CAQ 5VF sing 27 n y 
CAV CAS 5VF doub 28 n y 
CAQ CAR 5VF doub 29 n y 
CAS CAR 5VF sing 30 n y 
CAS CAT 5VF sing 31 n n 
CAT NAU 5VF sing 32 n n 
NAU CBE 5VF sing 33 n n 
NAU CBF 5VF sing 34 n n 
NBH CBF 5VF doub 35 n n 
CBF NBG 5VF sing 36 n n 
CAA H1 5VF sing 37 n n 
CAF H2 5VF sing 38 n n 
CAG H3 5VF sing 39 n n 
NAI H4 5VF sing 40 n n 
NAN H5 5VF sing 41 n n 
CAO H6 5VF sing 42 n n 
CAQ H7 5VF sing 43 n n 
CAR H8 5VF sing 44 n n 
CAT H9 5VF sing 45 n n 
CAT H10 5VF sing 46 n n 
CBE H11 5VF sing 47 n n 
CBE H12 5VF sing 48 n n 
CBE H13 5VF sing 49 n n 
NBH H14 5VF sing 50 n n 
NBG H15 5VF sing 51 n n 
NBG H16 5VF sing 52 n n 
CAV H17 5VF sing 53 n n 
CAX H18 5VF sing 54 n n 
CAX H19 5VF sing 55 n n 
CAY H20 5VF sing 56 n n 
CAZ H21 5VF sing 57 n n 
CAZ H22 5VF sing 58 n n 
NBA H23 5VF sing 59 n n 
NBD H24 5VF sing 60 n n 
NBC H25 5VF sing 61 n n 
NBC H26 5VF sing 62 n n 
#
_atom_sites.entry_id                     5F4R 
_atom_sites.fract_transf_matrix[1][1]    0.014776 
_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]    0.007852 
_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]    0.005207 
_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 FMT A 1 501 502 FMT FMT . 
D 3 NAG A 1 502 503 NAG NAG . 
E 3 NAG A 1 503 504 NAG NAG . 
F 3 NAG A 1 504 505 NAG NAG . 
G 3 NAG A 1 505 506 NAG NAG . 
H 3 NAG A 1 506 507 NAG NAG . 
I 3 NAG A 1 507 508 NAG NAG . 
J 4 5VF A 1 508 2 5VF DRG . 
K 2 FMT C 1 501 502 FMT FMT . 
L 3 NAG C 1 502 503 NAG NAG . 
M 3 NAG C 1 503 504 NAG NAG . 
N 3 NAG C 1 504 505 NAG NAG . 
O 3 NAG C 1 505 506 NAG NAG . 
P 3 NAG C 1 506 507 NAG NAG . 
Q 3 NAG C 1 507 508 NAG NAG . 
R 4 5VF C 1 508 1 5VF DRG . 
S 5 HOH A 1 601 3 HOH HOH . 
S 5 HOH A 2 602 34 HOH HOH . 
S 5 HOH A 3 603 11 HOH HOH . 
S 5 HOH A 4 604 25 HOH HOH . 
S 5 HOH A 5 605 29 HOH HOH . 
S 5 HOH A 6 606 15 HOH HOH . 
S 5 HOH A 7 607 30 HOH HOH . 
S 5 HOH A 8 608 2 HOH HOH . 
T 5 HOH C 1 601 7 HOH HOH . 
T 5 HOH C 2 602 33 HOH HOH . 
T 5 HOH C 3 603 4 HOH HOH . 
T 5 HOH C 4 604 31 HOH HOH . 
T 5 HOH C 5 605 16 HOH HOH . 
T 5 HOH C 6 606 1 HOH HOH . 
T 5 HOH C 7 607 5 HOH HOH . 
T 5 HOH C 8 608 14 HOH HOH . 
T 5 HOH C 9 609 21 HOH HOH . 
T 5 HOH C 10 610 6 HOH HOH . 
T 5 HOH C 11 611 28 HOH HOH . 
T 5 HOH C 12 612 8 HOH HOH . 
T 5 HOH C 13 613 27 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 CAA 5VF . . . J 4 -11.498 -53.462 18.178 1 90.5 ? CAA 5VF 508 A 1 
HETATM 2 C CAB 5VF . . . J 4 -10.971 -52.192 17.903 1 79.88 ? CAB 5VF 508 A 1 
HETATM 3 F FAC 5VF . . . J 4 -11.326 -51.136 18.682 1 88.18 ? FAC 5VF 508 A 1 
HETATM 4 C CAD 5VF . . . J 4 -10.074 -52.025 16.826 1 83.86 ? CAD 5VF 508 A 1 
HETATM 5 CL CLAE 5VF . . . J 4 -9.416 -50.499 16.461 1 172.39 ? CLAE 5VF 508 A 1 
HETATM 6 C CAF 5VF . . . J 4 -9.702 -53.112 16.024 1 84.64 ? CAF 5VF 508 A 1 
HETATM 7 C CAG 5VF . . . J 4 -10.232 -54.378 16.299 1 74.47 ? CAG 5VF 508 A 1 
HETATM 8 C CAH 5VF . . . J 4 -11.126 -54.55 17.369 1 79.76 ? CAH 5VF 508 A 1 
HETATM 9 N NAI 5VF . . . J 4 -11.652 -55.91 17.611 1 79.76 ? NAI 5VF 508 A 1 
HETATM 10 C CAJ 5VF . . . J 4 -12.977 -56.182 18.021 1 78.2 ? CAJ 5VF 508 A 1 
HETATM 11 O OAK 5VF . . . J 4 -13.77 -55.329 18.21 1 83.26 ? OAK 5VF 508 A 1 
HETATM 12 C CAL 5VF . . . J 4 -13.315 -57.621 18.204 1 73.57 ? CAL 5VF 508 A 1 
HETATM 13 O OAM 5VF . . . J 4 -12.444 -58.483 17.991 1 67.73 ? OAM 5VF 508 A 1 
HETATM 14 N NAN 5VF . . . J 4 -14.647 -58.054 18.628 1 75.61 ? NAN 5VF 508 A 1 
HETATM 15 C CAO 5VF . . . J 4 -14.849 -59.435 18.762 1 81.92 ? CAO 5VF 508 A 1 
HETATM 16 C CAP 5VF . . . J 4 -15.845 -59.682 19.847 1 85.19 ? CAP 5VF 508 A 1 
HETATM 17 C CAQ 5VF . . . J 4 -15.69 -59.685 21.257 1 86.93 ? CAQ 5VF 508 A 1 
HETATM 18 C CAR 5VF . . . J 4 -16.804 -59.945 22.064 1 85.86 ? CAR 5VF 508 A 1 
HETATM 19 C CAS 5VF . . . J 4 -18.061 -60.199 21.474 1 89.51 ? CAS 5VF 508 A 1 
HETATM 20 C CAT 5VF . . . J 4 -19.297 -60.487 22.368 1 92.84 ? CAT 5VF 508 A 1 
HETATM 21 N NAU 5VF . . . J 4 -19.359 -61.87 22.675 1 109.71 ? NAU 5VF 508 A 1 
HETATM 22 C CBE 5VF . . . J 4 -18.446 -62.783 22.13 1 91.88 ? CBE 5VF 508 A 1 
HETATM 23 C CBF 5VF . . . J 4 -20.336 -62.282 23.516 1 106.8 ? CBF 5VF 508 A 1 
HETATM 24 N NBH 5VF . . . J 4 -21.151 -61.432 24 1 103.63 ? NBH 5VF 508 A 1 
HETATM 25 N NBG 5VF . . . J 4 -20.436 -63.526 23.826 1 96.21 ? NBG 5VF 508 A 1 
HETATM 26 C CAV 5VF . . . J 4 -18.21 -60.193 20.076 1 82.53 ? CAV 5VF 508 A 1 
HETATM 27 C CAW 5VF . . . J 4 -17.094 -59.932 19.257 1 83.05 ? CAW 5VF 508 A 1 
HETATM 28 C CAX 5VF . . . J 4 -16.945 -59.868 17.729 1 81.54 ? CAX 5VF 508 A 1 
HETATM 29 C CAY 5VF . . . J 4 -15.475 -59.963 17.495 1 76.73 ? CAY 5VF 508 A 1 
HETATM 30 C CAZ 5VF . . . J 4 -15.069 -61.4 17.275 1 82.47 ? CAZ 5VF 508 A 1 
HETATM 31 N NBA 5VF . . . J 4 -14.196 -61.508 16.144 1 76.91 ? NBA 5VF 508 A 1 
HETATM 32 C CBB 5VF . . . J 4 -12.831 -62.021 16.265 1 74.46 ? CBB 5VF 508 A 1 
HETATM 33 N NBD 5VF . . . J 4 -12.089 -62.094 15.217 1 74.14 ? NBD 5VF 508 A 1 
HETATM 34 N NBC 5VF . . . J 4 -12.354 -62.407 17.446 1 79.79 ? NBC 5VF 508 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    79 
_model_server_stats.query_time_ms           564 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           34 
#