data_4V30
#
_model_server_result.job_id            zXHUI8rhenOfFkhPbEi75Q 
_model_server_result.datetime_utc      '2024-11-14 19:47:53' 
_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          4v30 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":151}' 
#
_entry.id    4V30 
#
_exptl.entry_id    4V30 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              259.261 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-Lenalidomide 
_entity.pdbx_number_of_molecules    3 
_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            4V30 
_cell.length_a            56.682 
_cell.length_b            59.743 
_cell.length_c            88.064 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4V30 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,J 1 1 
B,F,G,K 2 1 
C,H,I,L 3 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
? 3 E N N 
? 3 G N N 
? 3 I 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 25 A CYS 24 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
#
_chem_comp.formula           'C13 H13 N3 O3' 
_chem_comp.formula_weight    259.261 
_chem_comp.id                LVY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-Lenalidomide 
_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
C1 C2 LVY sing 194 n n 
C1 C6 LVY sing 195 n n 
C1 N10 LVY sing 196 n n 
C2 C3 LVY sing 197 n n 
C3 C4 LVY sing 198 n n 
C4 N5 LVY sing 199 n n 
C4 O19 LVY doub 200 n n 
N5 C6 LVY sing 201 n n 
C6 O18 LVY doub 202 n n 
C7 C8 LVY sing 203 n y 
C7 C11 LVY sing 204 n n 
C7 C15 LVY doub 205 n y 
C8 C9 LVY sing 206 n n 
C8 C14 LVY doub 207 n y 
C9 N10 LVY sing 208 n n 
N10 C11 LVY sing 209 n n 
C11 O16 LVY doub 210 n n 
C12 C13 LVY doub 211 n y 
C12 C15 LVY sing 212 n y 
C13 C14 LVY sing 213 n y 
C14 N17 LVY sing 214 n n 
C1 H1 LVY sing 215 n n 
C2 H21C LVY sing 216 n n 
C2 H22C LVY sing 217 n n 
C3 H31C LVY sing 218 n n 
C3 H32C LVY sing 219 n n 
N5 H5 LVY sing 220 n n 
C15 H15 LVY sing 221 n n 
C9 H91 LVY sing 222 n n 
C9 H92 LVY sing 223 n n 
C12 H12 LVY sing 224 n n 
C13 H13 LVY sing 225 n n 
N17 H171 LVY sing 226 n n 
N17 H172 LVY sing 227 n n 
#
_atom_sites.entry_id                     4V30 
_atom_sites.fract_transf_matrix[1][1]    0.017642 
_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]    0.016738 
_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]    0.011355 
_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
D 2 ZN A 1 150 150 ZN ZN . 
E 3 LVY A 1 151 151 LVY LVY . 
F 2 ZN B 1 150 150 ZN ZN . 
G 3 LVY B 1 151 151 LVY LVY . 
H 2 ZN C 1 150 150 ZN ZN . 
I 3 LVY C 1 151 151 LVY LVY . 
J 4 HOH A 1 2001 2001 HOH HOH . 
J 4 HOH A 2 2002 2002 HOH HOH . 
J 4 HOH A 3 2003 2003 HOH HOH . 
J 4 HOH A 4 2004 2004 HOH HOH . 
J 4 HOH A 5 2005 2005 HOH HOH . 
J 4 HOH A 6 2006 2006 HOH HOH . 
J 4 HOH A 7 2007 2007 HOH HOH . 
J 4 HOH A 8 2008 2008 HOH HOH . 
J 4 HOH A 9 2009 2009 HOH HOH . 
J 4 HOH A 10 2010 2010 HOH HOH . 
J 4 HOH A 11 2011 2011 HOH HOH . 
J 4 HOH A 12 2012 2012 HOH HOH . 
J 4 HOH A 13 2013 2013 HOH HOH . 
J 4 HOH A 14 2014 2014 HOH HOH . 
J 4 HOH A 15 2015 2015 HOH HOH . 
J 4 HOH A 16 2016 2016 HOH HOH . 
J 4 HOH A 17 2017 2017 HOH HOH . 
J 4 HOH A 18 2018 2018 HOH HOH . 
J 4 HOH A 19 2019 2019 HOH HOH . 
J 4 HOH A 20 2020 2020 HOH HOH . 
J 4 HOH A 21 2021 2021 HOH HOH . 
J 4 HOH A 22 2022 2022 HOH HOH . 
J 4 HOH A 23 2023 2023 HOH HOH . 
J 4 HOH A 24 2024 2024 HOH HOH . 
J 4 HOH A 25 2025 2025 HOH HOH . 
J 4 HOH A 26 2026 2026 HOH HOH . 
J 4 HOH A 27 2027 2027 HOH HOH . 
J 4 HOH A 28 2028 2028 HOH HOH . 
J 4 HOH A 29 2029 2029 HOH HOH . 
J 4 HOH A 30 2030 2030 HOH HOH . 
J 4 HOH A 31 2031 2031 HOH HOH . 
J 4 HOH A 32 2032 2032 HOH HOH . 
J 4 HOH A 33 2033 2033 HOH HOH . 
J 4 HOH A 34 2034 2034 HOH HOH . 
J 4 HOH A 35 2035 2035 HOH HOH . 
J 4 HOH A 36 2036 2036 HOH HOH . 
J 4 HOH A 37 2037 2037 HOH HOH . 
J 4 HOH A 38 2038 2038 HOH HOH . 
J 4 HOH A 39 2039 2039 HOH HOH . 
J 4 HOH A 40 2040 2040 HOH HOH . 
J 4 HOH A 41 2041 2041 HOH HOH . 
J 4 HOH A 42 2042 2042 HOH HOH . 
J 4 HOH A 43 2043 2043 HOH HOH . 
J 4 HOH A 44 2044 2044 HOH HOH . 
J 4 HOH A 45 2045 2045 HOH HOH . 
J 4 HOH A 46 2046 2046 HOH HOH . 
J 4 HOH A 47 2047 2047 HOH HOH . 
J 4 HOH A 48 2048 2048 HOH HOH . 
J 4 HOH A 49 2049 2049 HOH HOH . 
J 4 HOH A 50 2050 2050 HOH HOH . 
J 4 HOH A 51 2051 2051 HOH HOH . 
J 4 HOH A 52 2052 2052 HOH HOH . 
J 4 HOH A 53 2053 2053 HOH HOH . 
J 4 HOH A 54 2054 2054 HOH HOH . 
J 4 HOH A 55 2055 2055 HOH HOH . 
J 4 HOH A 56 2056 2056 HOH HOH . 
J 4 HOH A 57 2057 2057 HOH HOH . 
J 4 HOH A 58 2058 2058 HOH HOH . 
J 4 HOH A 59 2059 2059 HOH HOH . 
J 4 HOH A 60 2060 2060 HOH HOH . 
J 4 HOH A 61 2061 2061 HOH HOH . 
K 4 HOH B 1 2001 2001 HOH HOH . 
K 4 HOH B 2 2002 2002 HOH HOH . 
K 4 HOH B 3 2003 2003 HOH HOH . 
K 4 HOH B 4 2004 2004 HOH HOH . 
K 4 HOH B 5 2005 2005 HOH HOH . 
K 4 HOH B 6 2006 2006 HOH HOH . 
K 4 HOH B 7 2007 2007 HOH HOH . 
K 4 HOH B 8 2008 2008 HOH HOH . 
K 4 HOH B 9 2009 2009 HOH HOH . 
K 4 HOH B 10 2010 2010 HOH HOH . 
K 4 HOH B 11 2011 2011 HOH HOH . 
K 4 HOH B 12 2012 2012 HOH HOH . 
K 4 HOH B 13 2013 2013 HOH HOH . 
K 4 HOH B 14 2014 2014 HOH HOH . 
K 4 HOH B 15 2015 2015 HOH HOH . 
K 4 HOH B 16 2016 2016 HOH HOH . 
K 4 HOH B 17 2017 2017 HOH HOH . 
K 4 HOH B 18 2018 2018 HOH HOH . 
K 4 HOH B 19 2019 2019 HOH HOH . 
K 4 HOH B 20 2020 2020 HOH HOH . 
K 4 HOH B 21 2021 2021 HOH HOH . 
K 4 HOH B 22 2022 2022 HOH HOH . 
K 4 HOH B 23 2023 2023 HOH HOH . 
K 4 HOH B 24 2024 2024 HOH HOH . 
K 4 HOH B 25 2025 2025 HOH HOH . 
K 4 HOH B 26 2026 2026 HOH HOH . 
K 4 HOH B 27 2027 2027 HOH HOH . 
K 4 HOH B 28 2028 2028 HOH HOH . 
K 4 HOH B 29 2029 2029 HOH HOH . 
K 4 HOH B 30 2030 2030 HOH HOH . 
K 4 HOH B 31 2031 2031 HOH HOH . 
K 4 HOH B 32 2032 2032 HOH HOH . 
K 4 HOH B 33 2033 2033 HOH HOH . 
K 4 HOH B 34 2034 2034 HOH HOH . 
K 4 HOH B 35 2035 2035 HOH HOH . 
K 4 HOH B 36 2036 2036 HOH HOH . 
K 4 HOH B 37 2037 2037 HOH HOH . 
K 4 HOH B 38 2038 2038 HOH HOH . 
K 4 HOH B 39 2039 2039 HOH HOH . 
K 4 HOH B 40 2040 2040 HOH HOH . 
K 4 HOH B 41 2041 2041 HOH HOH . 
K 4 HOH B 42 2042 2042 HOH HOH . 
K 4 HOH B 43 2043 2043 HOH HOH . 
K 4 HOH B 44 2044 2044 HOH HOH . 
K 4 HOH B 45 2045 2045 HOH HOH . 
K 4 HOH B 46 2046 2046 HOH HOH . 
K 4 HOH B 47 2047 2047 HOH HOH . 
K 4 HOH B 48 2048 2048 HOH HOH . 
K 4 HOH B 49 2049 2049 HOH HOH . 
K 4 HOH B 50 2050 2050 HOH HOH . 
K 4 HOH B 51 2051 2051 HOH HOH . 
K 4 HOH B 52 2052 2052 HOH HOH . 
K 4 HOH B 53 2053 2053 HOH HOH . 
K 4 HOH B 54 2054 2054 HOH HOH . 
K 4 HOH B 55 2055 2055 HOH HOH . 
K 4 HOH B 56 2056 2056 HOH HOH . 
K 4 HOH B 57 2057 2057 HOH HOH . 
K 4 HOH B 58 2058 2058 HOH HOH . 
K 4 HOH B 59 2059 2059 HOH HOH . 
K 4 HOH B 60 2060 2060 HOH HOH . 
K 4 HOH B 61 2061 2061 HOH HOH . 
K 4 HOH B 62 2062 2062 HOH HOH . 
L 4 HOH C 1 2001 2001 HOH HOH . 
L 4 HOH C 2 2002 2002 HOH HOH . 
L 4 HOH C 3 2003 2003 HOH HOH . 
L 4 HOH C 4 2004 2004 HOH HOH . 
L 4 HOH C 5 2005 2005 HOH HOH . 
L 4 HOH C 6 2006 2006 HOH HOH . 
L 4 HOH C 7 2007 2007 HOH HOH . 
L 4 HOH C 8 2008 2008 HOH HOH . 
L 4 HOH C 9 2009 2009 HOH HOH . 
L 4 HOH C 10 2010 2010 HOH HOH . 
L 4 HOH C 11 2011 2011 HOH HOH . 
L 4 HOH C 12 2012 2012 HOH HOH . 
L 4 HOH C 13 2013 2013 HOH HOH . 
L 4 HOH C 14 2014 2014 HOH HOH . 
L 4 HOH C 15 2015 2015 HOH HOH . 
L 4 HOH C 16 2016 2016 HOH HOH . 
L 4 HOH C 17 2017 2017 HOH HOH . 
L 4 HOH C 18 2018 2018 HOH HOH . 
L 4 HOH C 19 2019 2019 HOH HOH . 
L 4 HOH C 20 2020 2020 HOH HOH . 
L 4 HOH C 21 2021 2021 HOH HOH . 
L 4 HOH C 22 2022 2022 HOH HOH . 
L 4 HOH C 23 2023 2023 HOH HOH . 
L 4 HOH C 24 2024 2024 HOH HOH . 
L 4 HOH C 25 2025 2025 HOH HOH . 
L 4 HOH C 26 2026 2026 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 LVY . . . E 3 25.158 18.095 -7.418 1 27.26 ? C1 LVY 151 A 1 
HETATM 2 C C2 LVY . . . E 3 23.855 18.852 -7.437 1 25.96 ? C2 LVY 151 A 1 
HETATM 3 C C3 LVY . . . E 3 22.844 17.886 -6.841 1 25.04 ? C3 LVY 151 A 1 
HETATM 4 C C4 LVY . . . E 3 22.715 16.596 -7.607 1 25.99 ? C4 LVY 151 A 1 
HETATM 5 N N5 LVY . . . E 3 23.783 16.15 -8.215 1 27.11 ? N5 LVY 151 A 1 
HETATM 6 C C6 LVY . . . E 3 24.997 16.776 -8.173 1 28.13 ? C6 LVY 151 A 1 
HETATM 7 C C7 LVY . . . E 3 28.349 19.864 -8.192 1 33.46 ? C7 LVY 151 A 1 
HETATM 8 C C8 LVY . . . E 3 27.747 19.868 -9.42 1 33.82 ? C8 LVY 151 A 1 
HETATM 9 C C9 LVY . . . E 3 26.415 19.222 -9.435 1 31.67 ? C9 LVY 151 A 1 
HETATM 10 N N10 LVY . . . E 3 26.309 18.839 -8.032 1 29.63 ? N10 LVY 151 A 1 
HETATM 11 C C11 LVY . . . E 3 27.359 19.191 -7.359 1 30.42 ? C11 LVY 151 A 1 
HETATM 12 C C12 LVY . . . E 3 30.273 20.95 -8.938 1 38.33 ? C12 LVY 151 A 1 
HETATM 13 C C13 LVY . . . E 3 29.75 20.958 -10.232 1 38.99 ? C13 LVY 151 A 1 
HETATM 14 C C14 LVY . . . E 3 28.476 20.436 -10.48 1 37.26 ? C14 LVY 151 A 1 
HETATM 15 C C15 LVY . . . E 3 29.598 20.404 -7.898 1 35.4 ? C15 LVY 151 A 1 
HETATM 16 O O16 LVY . . . E 3 27.433 18.939 -5.96 1 28.14 ? O16 LVY 151 A 1 
HETATM 17 N N17 LVY . . . E 3 28.038 20.484 -11.763 1 38.32 ? N17 LVY 151 A 1 
HETATM 18 O O18 LVY . . . E 3 25.957 16.295 -8.762 1 29.84 ? O18 LVY 151 A 1 
HETATM 19 O O19 LVY . . . E 3 21.638 15.981 -7.593 1 26.9 ? O19 LVY 151 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           19 
#