data_3CLX
#
_model_server_result.job_id            l9adNuOF_ntJzPipIrSAOQ 
_model_server_result.datetime_utc      '2025-02-05 12:53:33' 
_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          3clx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":600}' 
#
_entry.id    3CLX 
#
_exptl.entry_id    3CLX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              492.61 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide 
_entity.pdbx_number_of_molecules    6 
_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            3CLX 
_cell.length_a            64.875 
_cell.length_b            115.28 
_cell.length_c            163.233 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CLX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA dimeric 2 software_defined_assembly 5 
PISA dimeric 2 software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
B,G,H,P 1 1 
C,I,J,Q 2 1 
D,K,L,M,N,R 3 1 
A,E,F,O 4 1 
B,D,G,H,K,L,M,N,P,R 5 1 
A,E,F,O 6 2 
C,I,J,Q 6 1 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -81.6165 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
? 3 M N N 
? 3 N 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 B SG CYS 125 A CYS 351 1_555 D SG CYS 125 C CYS 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? 
metalc ? metalc1 A SG CYS 74 D CYS 300 1_555 E ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc2 A SG CYS 77 D CYS 303 1_555 E ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc3 A NE2 HIS 94 D HIS 320 1_555 E ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc4 A SG CYS 101 D CYS 327 1_555 E ZN ZN . D ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc5 B SG CYS 74 A CYS 300 1_555 G ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc6 B SG CYS 77 A CYS 303 1_555 G ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc7 B NE2 HIS 94 A HIS 320 1_555 G ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc8 B SG CYS 101 A CYS 327 1_555 G ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc9 C SG CYS 74 B CYS 300 1_555 I ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc10 C SG CYS 77 B CYS 303 1_555 I ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc11 C NE2 HIS 94 B HIS 320 1_555 I ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc12 C SG CYS 101 B CYS 327 1_555 I ZN ZN . B ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc13 D SG CYS 74 C CYS 300 1_555 K ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc14 D SG CYS 77 C CYS 303 1_555 K ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
metalc ? metalc15 D NE2 HIS 94 C HIS 320 1_555 K ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc16 D SG CYS 101 C CYS 327 1_555 K ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
#
_chem_comp.formula           'C28 H36 N4 O4' 
_chem_comp.formula_weight    492.61 
_chem_comp.id                X22 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '2(S),3(S),6(S),7(S),9a(S) 6-(2-Amino-butyrylamino)-7-hydroxymethyl-5-oxo-octahydro-pyrrolo[1,2-a]azepine-3-carboxylic acid benzhydryl-amide' 
#
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 CB X22 sing 376 n n 
CB CA X22 sing 377 n n 
CA N X22 sing 378 n n 
CA C X22 sing 379 n n 
C O X22 doub 380 n n 
C NAX X22 sing 381 n n 
NAX CBI X22 sing 382 n n 
CBI CBA X22 sing 383 n n 
CBI CBE X22 sing 384 n n 
CBA OAE X22 doub 385 n n 
CBA NBJ X22 sing 386 n n 
NBJ CBF X22 sing 387 n n 
NBJ CBG X22 sing 388 n n 
CBE CAR X22 sing 389 n n 
CBE CAS X22 sing 390 n n 
CAR OAF X22 sing 391 n n 
CAS CAT X22 sing 392 n n 
CAT CBF X22 sing 393 n n 
CBF CAU X22 sing 394 n n 
CAU CAV X22 sing 395 n n 
CAV CBG X22 sing 396 n n 
CBG CAZ X22 sing 397 n n 
CAZ OAD X22 doub 398 n n 
CAZ NAW X22 sing 399 n n 
NAW CBH X22 sing 400 n n 
CBH CBC X22 sing 401 n n 
CBH CBB X22 sing 402 n n 
CBC CAO X22 doub 403 n y 
CBC CAP X22 sing 404 n y 
CAO CAK X22 sing 405 n y 
CAK CAH X22 doub 406 n y 
CAH CAL X22 sing 407 n y 
CAL CAP X22 doub 408 n y 
CBB CAM X22 doub 409 n y 
CBB CAN X22 sing 410 n y 
CAM CAI X22 sing 411 n y 
CAI CAG X22 doub 412 n y 
CAG CAJ X22 sing 413 n y 
CAJ CAN X22 doub 414 n y 
CAA HAA X22 sing 415 n n 
CAA HAAA X22 sing 416 n n 
CAA HAAB X22 sing 417 n n 
CB HB X22 sing 418 n n 
CB HBA X22 sing 419 n n 
CA HA X22 sing 420 n n 
N HN X22 sing 421 n n 
N HNA X22 sing 422 n n 
NAX HNAX X22 sing 423 n n 
CBI HBI X22 sing 424 n n 
CBE HBE X22 sing 425 n n 
CAR HAR X22 sing 426 n n 
CAR HARA X22 sing 427 n n 
OAF HOAF X22 sing 428 n n 
CAS HAS X22 sing 429 n n 
CAS HASA X22 sing 430 n n 
CAT HAT X22 sing 431 n n 
CAT HATA X22 sing 432 n n 
CBF HBF X22 sing 433 n n 
CAU HAU X22 sing 434 n n 
CAU HAUA X22 sing 435 n n 
CAV HAV X22 sing 436 n n 
CAV HAVA X22 sing 437 n n 
CBG HBG X22 sing 438 n n 
NAW HNAW X22 sing 439 n n 
CBH HBH X22 sing 440 n n 
CAO HAO X22 sing 441 n n 
CAK HAK X22 sing 442 n n 
CAH HAH X22 sing 443 n n 
CAL HAL X22 sing 444 n n 
CAP HAP X22 sing 445 n n 
CAM HAM X22 sing 446 n n 
CAI HAI X22 sing 447 n n 
CAG HAG X22 sing 448 n n 
CAJ HAJ X22 sing 449 n n 
CAN HAN X22 sing 450 n n 
#
_atom_sites.entry_id                     3CLX 
_atom_sites.fract_transf_matrix[1][1]    0.015414 
_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]    0.008675 
_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]    0.006126 
_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 2 ZN D 1 502 502 ZN ZN . 
F 3 X22 D 1 600 600 X22 X22 . 
G 2 ZN A 1 502 502 ZN ZN . 
H 3 X22 A 1 600 600 X22 X22 . 
I 2 ZN B 1 502 502 ZN ZN . 
J 3 X22 B 1 600 600 X22 X22 . 
K 2 ZN C 1 502 502 ZN ZN . 
L 3 X22 C 1 700 700 X22 X22 . 
M 3 X22 C 1 600 600 X22 X22 . 
N 3 X22 C 1 701 701 X22 X22 . 
O 4 HOH D 1 7 7 HOH HOH . 
O 4 HOH D 2 10 10 HOH HOH . 
O 4 HOH D 3 11 11 HOH HOH . 
O 4 HOH D 4 12 12 HOH HOH . 
O 4 HOH D 5 13 13 HOH HOH . 
O 4 HOH D 6 19 19 HOH HOH . 
O 4 HOH D 7 23 23 HOH HOH . 
O 4 HOH D 8 24 24 HOH HOH . 
O 4 HOH D 9 32 32 HOH HOH . 
O 4 HOH D 10 33 33 HOH HOH . 
O 4 HOH D 11 34 34 HOH HOH . 
O 4 HOH D 12 42 42 HOH HOH . 
O 4 HOH D 13 49 49 HOH HOH . 
O 4 HOH D 14 53 53 HOH HOH . 
O 4 HOH D 15 54 54 HOH HOH . 
P 4 HOH A 1 4 4 HOH HOH . 
P 4 HOH A 2 6 6 HOH HOH . 
P 4 HOH A 3 15 15 HOH HOH . 
P 4 HOH A 4 17 17 HOH HOH . 
P 4 HOH A 5 21 21 HOH HOH . 
P 4 HOH A 6 26 26 HOH HOH . 
P 4 HOH A 7 36 36 HOH HOH . 
P 4 HOH A 8 43 43 HOH HOH . 
P 4 HOH A 9 47 47 HOH HOH . 
P 4 HOH A 10 50 50 HOH HOH . 
Q 4 HOH B 1 1 1 HOH HOH . 
Q 4 HOH B 2 5 5 HOH HOH . 
Q 4 HOH B 3 8 8 HOH HOH . 
Q 4 HOH B 4 9 9 HOH HOH . 
Q 4 HOH B 5 18 18 HOH HOH . 
Q 4 HOH B 6 29 29 HOH HOH . 
Q 4 HOH B 7 40 40 HOH HOH . 
Q 4 HOH B 8 48 48 HOH HOH . 
R 4 HOH C 1 3 3 HOH HOH . 
R 4 HOH C 2 14 14 HOH HOH . 
R 4 HOH C 3 16 16 HOH HOH . 
R 4 HOH C 4 20 20 HOH HOH . 
R 4 HOH C 5 25 25 HOH HOH . 
R 4 HOH C 6 27 27 HOH HOH . 
R 4 HOH C 7 28 28 HOH HOH . 
R 4 HOH C 8 31 31 HOH HOH . 
R 4 HOH C 9 35 35 HOH HOH . 
R 4 HOH C 10 37 37 HOH HOH . 
R 4 HOH C 11 38 38 HOH HOH . 
R 4 HOH C 12 41 41 HOH HOH . 
R 4 HOH C 13 45 45 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 X22 . . . J 3 -12.168 44.2 -33.204 1 41.54 ? CAA X22 600 B 1 
HETATM 2 C CB X22 . . . J 3 -13.199 45.235 -32.766 1 41.62 ? CB X22 600 B 1 
HETATM 3 C CA X22 . . . J 3 -12.676 46.678 -32.596 1 41.69 ? CA X22 600 B 1 
HETATM 4 N N X22 . . . J 3 -13.158 47.51 -33.699 1 42.6 ? N X22 600 B 1 
HETATM 5 C C X22 . . . J 3 -11.153 46.809 -32.499 1 42.48 ? C X22 600 B 1 
HETATM 6 O O X22 . . . J 3 -10.427 46.729 -33.492 1 42.61 ? O X22 600 B 1 
HETATM 7 N NAX X22 . . . J 3 -10.721 47.046 -31.266 1 43.85 ? NAX X22 600 B 1 
HETATM 8 C CBI X22 . . . J 3 -9.295 47.213 -30.947 1 45.13 ? CBI X22 600 B 1 
HETATM 9 C CBA X22 . . . J 3 -8.804 46.059 -30.024 1 42.57 ? CBA X22 600 B 1 
HETATM 10 O OAE X22 . . . J 3 -9.629 45.238 -29.617 1 35.2 ? OAE X22 600 B 1 
HETATM 11 N NBJ X22 . . . J 3 -7.512 45.898 -29.678 1 44.29 ? NBJ X22 600 B 1 
HETATM 12 C CBE X22 . . . J 3 -9.014 48.671 -30.465 1 48.15 ? CBE X22 600 B 1 
HETATM 13 C CAR X22 . . . J 3 -9.774 49.074 -29.189 1 54.65 ? CAR X22 600 B 1 
HETATM 14 O OAF X22 . . . J 3 -11.019 49.681 -29.571 1 62.34 ? OAF X22 600 B 1 
HETATM 15 C CAS X22 . . . J 3 -7.505 49.036 -30.381 1 49.12 ? CAS X22 600 B 1 
HETATM 16 C CAT X22 . . . J 3 -6.621 48.145 -29.486 1 43.62 ? CAT X22 600 B 1 
HETATM 17 C CBF X22 . . . J 3 -6.392 46.761 -30.099 1 40.99 ? CBF X22 600 B 1 
HETATM 18 C CAU X22 . . . J 3 -5.131 46.143 -29.5 1 42.28 ? CAU X22 600 B 1 
HETATM 19 C CAV X22 . . . J 3 -5.521 44.699 -29.213 1 44.87 ? CAV X22 600 B 1 
HETATM 20 C CBG X22 . . . J 3 -7.012 44.772 -28.849 1 46.58 ? CBG X22 600 B 1 
HETATM 21 C CAZ X22 . . . J 3 -7.162 44.86 -27.305 1 52.4 ? CAZ X22 600 B 1 
HETATM 22 O OAD X22 . . . J 3 -7.709 45.801 -26.726 1 54.36 ? OAD X22 600 B 1 
HETATM 23 N NAW X22 . . . J 3 -6.629 43.772 -26.733 1 57.11 ? NAW X22 600 B 1 
HETATM 24 C CBH X22 . . . J 3 -6.483 43.342 -25.309 1 54.62 ? CBH X22 600 B 1 
HETATM 25 C CBC X22 . . . J 3 -6.051 44.425 -24.308 1 52.31 ? CBC X22 600 B 1 
HETATM 26 C CAO X22 . . . J 3 -4.679 44.626 -24.127 1 48.86 ? CAO X22 600 B 1 
HETATM 27 C CAK X22 . . . J 3 -4.214 45.579 -23.227 1 45.74 ? CAK X22 600 B 1 
HETATM 28 C CAH X22 . . . J 3 -5.133 46.323 -22.497 1 49.95 ? CAH X22 600 B 1 
HETATM 29 C CAL X22 . . . J 3 -6.506 46.117 -22.664 1 54.28 ? CAL X22 600 B 1 
HETATM 30 C CAP X22 . . . J 3 -6.974 45.165 -23.571 1 54.27 ? CAP X22 600 B 1 
HETATM 31 C CBB X22 . . . J 3 -7.64 42.442 -24.805 1 59.03 ? CBB X22 600 B 1 
HETATM 32 C CAM X22 . . . J 3 -7.405 41.602 -23.709 1 58.8 ? CAM X22 600 B 1 
HETATM 33 C CAI X22 . . . J 3 -8.411 40.76 -23.236 1 55.51 ? CAI X22 600 B 1 
HETATM 34 C CAG X22 . . . J 3 -9.65 40.744 -23.869 1 53.14 ? CAG X22 600 B 1 
HETATM 35 C CAJ X22 . . . J 3 -9.883 41.568 -24.968 1 53.55 ? CAJ X22 600 B 1 
HETATM 36 C CAN X22 . . . J 3 -8.882 42.415 -25.441 1 55.65 ? CAN X22 600 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#