data_6PVS # _model_server_result.job_id X25z5gYuO0N9pBzf8smpYw _model_server_result.datetime_utc '2025-02-20 11:34:11' _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 6pvs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 6PVS # _exptl.entry_id 6PVS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 524.529 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-(5-{[(3R)-3-amino-3-carboxypropyl][3-(3-carbamoylphenyl)prop-2-yn-1-yl]amino}-5-deoxy-alpha-D-lyxofuranosyl)-9H-purin-6-amine _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 82.72 _cell.angle_beta 82.48 _cell.angle_gamma 68.34 _cell.entry_id 6PVS _cell.length_a 46.23 _cell.length_b 62.53 _cell.length_c 108.359 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PVS _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C24 H28 N8 O6' _chem_comp.formula_weight 524.529 _chem_comp.id P0V _chem_comp.mon_nstd_flag . _chem_comp.name 9-(5-{[(3R)-3-amino-3-carboxypropyl][3-(3-carbamoylphenyl)prop-2-yn-1-yl]amino}-5-deoxy-alpha-D-lyxofuranosyl)-9H-purin-6-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 N17 C6 P0V sing 237 n n N7 C8 P0V doub 238 n y N7 C1 P0V sing 239 n y C8 N9 P0V sing 240 n y C1 C6 P0V doub 241 n y C1 C2 P0V sing 242 n y C6 N5 P0V sing 243 n y N9 C2 P0V sing 244 n y N9 C10 P0V sing 245 n n N5 C4 P0V doub 246 n y C2 N3 P0V doub 247 n y C10 C14 P0V sing 248 n n C10 O11 P0V sing 249 n n O23 C14 P0V sing 250 n n O35 C33 P0V doub 251 n n C4 N3 P0V sing 252 n y C14 C13 P0V sing 253 n n O11 C12 P0V sing 254 n n C33 N34 P0V sing 255 n n C33 C29 P0V sing 256 n n C15 C12 P0V sing 257 n n C15 N16 P0V sing 258 n n O22 C13 P0V sing 259 n n C28 C29 P0V doub 260 n y C28 C27 P0V sing 261 n y C13 C12 P0V sing 262 n n C29 C30 P0V sing 263 n y C24 C25 P0V sing 264 n n C24 N16 P0V sing 265 n n C25 C26 P0V trip 266 n n C26 C27 P0V sing 267 n n N16 C18 P0V sing 268 n n C27 C32 P0V doub 269 n y C30 C31 P0V doub 270 n y C32 C31 P0V sing 271 n y C18 C19 P0V sing 272 n n C19 C20 P0V sing 273 n n C20 N21 P0V sing 274 n n C20 C36 P0V sing 275 n n O38 C36 P0V doub 276 n n C36 O37 P0V sing 277 n n C28 H281 P0V sing 278 n n C30 H301 P0V sing 279 n n C19 H192 P0V sing 280 n n C19 H191 P0V sing 281 n n C14 H141 P0V sing 282 n n C15 H152 P0V sing 283 n n C15 H151 P0V sing 284 n n C13 H131 P0V sing 285 n n C12 H121 P0V sing 286 n n C4 H41 P0V sing 287 n n C8 H81 P0V sing 288 n n C10 H101 P0V sing 289 n n C18 H182 P0V sing 290 n n C18 H181 P0V sing 291 n n C20 H201 P0V sing 292 n n C24 H242 P0V sing 293 n n C24 H241 P0V sing 294 n n C31 H311 P0V sing 295 n n C32 H321 P0V sing 296 n n N17 H172 P0V sing 297 n n N17 H171 P0V sing 298 n n N21 H211 P0V sing 299 n n N21 H212 P0V sing 300 n n N34 H341 P0V sing 301 n n N34 H342 P0V sing 302 n n O22 H221 P0V sing 303 n n O23 H231 P0V sing 304 n n O37 H3 P0V sing 305 n n # _atom_sites.entry_id 6PVS _atom_sites.fract_transf_matrix[1][1] 0.021631 _atom_sites.fract_transf_matrix[1][2] -0.008592 _atom_sites.fract_transf_matrix[1][3] -0.002132 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017208 _atom_sites.fract_transf_matrix[2][3] -0.001469 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009343 _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 P0V A 1 301 301 P0V 320 . F 2 P0V B 1 301 301 P0V 320 . G 2 P0V C 1 301 301 P0V 320 . H 2 P0V D 1 301 301 P0V 320 . I 3 HOH A 1 401 45 HOH HOH . I 3 HOH A 2 402 26 HOH HOH . I 3 HOH A 3 403 10 HOH HOH . I 3 HOH A 4 404 5 HOH HOH . I 3 HOH A 5 405 50 HOH HOH . I 3 HOH A 6 406 57 HOH HOH . I 3 HOH A 7 407 63 HOH HOH . I 3 HOH A 8 408 22 HOH HOH . I 3 HOH A 9 409 12 HOH HOH . I 3 HOH A 10 410 14 HOH HOH . I 3 HOH A 11 411 39 HOH HOH . I 3 HOH A 12 412 73 HOH HOH . I 3 HOH A 13 413 40 HOH HOH . I 3 HOH A 14 414 55 HOH HOH . I 3 HOH A 15 415 27 HOH HOH . I 3 HOH A 16 416 101 HOH HOH . I 3 HOH A 17 417 19 HOH HOH . I 3 HOH A 18 418 98 HOH HOH . I 3 HOH A 19 419 47 HOH HOH . I 3 HOH A 20 420 69 HOH HOH . I 3 HOH A 21 421 89 HOH HOH . I 3 HOH A 22 422 107 HOH HOH . I 3 HOH A 23 423 93 HOH HOH . I 3 HOH A 24 424 4 HOH HOH . I 3 HOH A 25 425 104 HOH HOH . I 3 HOH A 26 426 70 HOH HOH . I 3 HOH A 27 427 105 HOH HOH . I 3 HOH A 28 428 106 HOH HOH . J 3 HOH B 1 401 84 HOH HOH . J 3 HOH B 2 402 71 HOH HOH . J 3 HOH B 3 403 99 HOH HOH . J 3 HOH B 4 404 80 HOH HOH . J 3 HOH B 5 405 88 HOH HOH . J 3 HOH B 6 406 92 HOH HOH . J 3 HOH B 7 407 68 HOH HOH . J 3 HOH B 8 408 59 HOH HOH . J 3 HOH B 9 409 62 HOH HOH . J 3 HOH B 10 410 103 HOH HOH . J 3 HOH B 11 411 15 HOH HOH . J 3 HOH B 12 412 16 HOH HOH . J 3 HOH B 13 413 32 HOH HOH . J 3 HOH B 14 414 31 HOH HOH . J 3 HOH B 15 415 8 HOH HOH . J 3 HOH B 16 416 64 HOH HOH . J 3 HOH B 17 417 49 HOH HOH . J 3 HOH B 18 418 67 HOH HOH . J 3 HOH B 19 419 102 HOH HOH . J 3 HOH B 20 420 29 HOH HOH . J 3 HOH B 21 421 82 HOH HOH . J 3 HOH B 22 422 60 HOH HOH . J 3 HOH B 23 423 81 HOH HOH . J 3 HOH B 24 424 36 HOH HOH . J 3 HOH B 25 425 2 HOH HOH . J 3 HOH B 26 426 90 HOH HOH . J 3 HOH B 27 427 61 HOH HOH . J 3 HOH B 28 428 56 HOH HOH . J 3 HOH B 29 429 13 HOH HOH . J 3 HOH B 30 430 108 HOH HOH . J 3 HOH B 31 431 96 HOH HOH . K 3 HOH C 1 401 18 HOH HOH . K 3 HOH C 2 402 28 HOH HOH . K 3 HOH C 3 403 46 HOH HOH . K 3 HOH C 4 404 53 HOH HOH . K 3 HOH C 5 405 75 HOH HOH . K 3 HOH C 6 406 54 HOH HOH . K 3 HOH C 7 407 77 HOH HOH . K 3 HOH C 8 408 17 HOH HOH . K 3 HOH C 9 409 100 HOH HOH . K 3 HOH C 10 410 35 HOH HOH . K 3 HOH C 11 411 6 HOH HOH . K 3 HOH C 12 412 3 HOH HOH . K 3 HOH C 13 413 42 HOH HOH . K 3 HOH C 14 414 48 HOH HOH . K 3 HOH C 15 415 52 HOH HOH . K 3 HOH C 16 416 20 HOH HOH . K 3 HOH C 17 417 83 HOH HOH . K 3 HOH C 18 418 23 HOH HOH . K 3 HOH C 19 419 110 HOH HOH . K 3 HOH C 20 420 95 HOH HOH . K 3 HOH C 21 421 79 HOH HOH . K 3 HOH C 22 422 37 HOH HOH . K 3 HOH C 23 423 72 HOH HOH . K 3 HOH C 24 424 109 HOH HOH . K 3 HOH C 25 425 111 HOH HOH . K 3 HOH C 26 426 86 HOH HOH . K 3 HOH C 27 427 87 HOH HOH . K 3 HOH C 28 428 65 HOH HOH . K 3 HOH C 29 429 78 HOH HOH . L 3 HOH D 1 401 24 HOH HOH . L 3 HOH D 2 402 91 HOH HOH . L 3 HOH D 3 403 9 HOH HOH . L 3 HOH D 4 404 33 HOH HOH . L 3 HOH D 5 405 58 HOH HOH . L 3 HOH D 6 406 74 HOH HOH . L 3 HOH D 7 407 7 HOH HOH . L 3 HOH D 8 408 1 HOH HOH . L 3 HOH D 9 409 85 HOH HOH . L 3 HOH D 10 410 21 HOH HOH . L 3 HOH D 11 411 43 HOH HOH . L 3 HOH D 12 412 11 HOH HOH . L 3 HOH D 13 413 94 HOH HOH . L 3 HOH D 14 414 25 HOH HOH . L 3 HOH D 15 415 34 HOH HOH . L 3 HOH D 16 416 30 HOH HOH . L 3 HOH D 17 417 38 HOH HOH . L 3 HOH D 18 418 41 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 C28 P0V . . . G 2 -19.101 -27.556 18.655 1 39.81 ? C28 P0V 301 C 1 HETATM 2 C C29 P0V . . . G 2 -20.051 -27.889 17.673 1 41.72 ? C29 P0V 301 C 1 HETATM 3 C C30 P0V . . . G 2 -21.059 -28.795 17.961 1 44.21 ? C30 P0V 301 C 1 HETATM 4 C C27 P0V . . . G 2 -19.125 -28.21 19.877 1 42.09 ? C27 P0V 301 C 1 HETATM 5 C C26 P0V . . . G 2 -18.073 -27.907 20.945 1 41.67 ? C26 P0V 301 C 1 HETATM 6 C C19 P0V . . . G 2 -14.898 -30.125 22.666 1 41.39 ? C19 P0V 301 C 1 HETATM 7 C C14 P0V . . . G 2 -10.918 -25.157 23.599 1 49.19 ? C14 P0V 301 C 1 HETATM 8 C C15 P0V . . . G 2 -13.97 -26.391 22.396 1 48.85 ? C15 P0V 301 C 1 HETATM 9 C C13 P0V . . . G 2 -11.967 -26.169 23.866 1 47.29 ? C13 P0V 301 C 1 HETATM 10 C C12 P0V . . . G 2 -12.489 -26.615 22.551 1 46.59 ? C12 P0V 301 C 1 HETATM 11 C C6 P0V . . . G 2 -7.224 -23.216 20.469 1 47.15 ? C6 P0V 301 C 1 HETATM 12 C C4 P0V . . . G 2 -7.023 -25.072 21.872 1 50.65 ? C4 P0V 301 C 1 HETATM 13 N N3 P0V . . . G 2 -8.32 -25.067 22.136 1 51.45 ? N3 P0V 301 C 1 HETATM 14 C C2 P0V . . . G 2 -9.132 -24.149 21.59 1 50.44 ? C2 P0V 301 C 1 HETATM 15 C C1 P0V . . . G 2 -8.578 -23.178 20.721 1 50.05 ? C1 P0V 301 C 1 HETATM 16 N N9 P0V . . . G 2 -10.322 -23.831 21.592 1 54.27 ? N9 P0V 301 C 1 HETATM 17 C C8 P0V . . . G 2 -10.761 -22.879 20.944 1 54.66 ? C8 P0V 301 C 1 HETATM 18 C C10 P0V . . . G 2 -11.301 -24.546 22.326 1 48.95 ? C10 P0V 301 C 1 HETATM 19 C C18 P0V . . . G 2 -14.227 -28.795 23.113 1 44.12 ? C18 P0V 301 C 1 HETATM 20 C C20 P0V . . . G 2 -14.004 -31.299 23.008 1 43.42 ? C20 P0V 301 C 1 HETATM 21 C C24 P0V . . . G 2 -16.167 -27.357 22.859 1 45.36 ? C24 P0V 301 C 1 HETATM 22 C C25 P0V . . . G 2 -17.236 -27.662 21.776 1 43.07 ? C25 P0V 301 C 1 HETATM 23 C C31 P0V . . . G 2 -21.088 -29.438 19.2 1 43.49 ? C31 P0V 301 C 1 HETATM 24 C C32 P0V . . . G 2 -20.116 -29.145 20.162 1 43.4 ? C32 P0V 301 C 1 HETATM 25 C C33 P0V . . . G 2 -20.032 -27.149 16.324 1 44.33 ? C33 P0V 301 C 1 HETATM 26 C C36 P0V . . . G 2 -14.84 -32.586 22.679 1 40.97 ? C36 P0V 301 C 1 HETATM 27 N N16 P0V . . . G 2 -14.792 -27.652 22.318 1 46.81 ? N16 P0V 301 C 1 HETATM 28 N N17 P0V . . . G 2 -6.631 -22.243 19.58 1 49.59 ? N17 P0V 301 C 1 HETATM 29 N N21 P0V . . . G 2 -13.59 -31.28 24.392 1 46.52 ? N21 P0V 301 C 1 HETATM 30 N N34 P0V . . . G 2 -18.775 -27.102 15.545 1 47.06 ? N34 P0V 301 C 1 HETATM 31 N N5 P0V . . . G 2 -6.479 -24.162 21.05 1 47.64 ? N5 P0V 301 C 1 HETATM 32 N N7 P0V . . . G 2 -9.703 -22.37 20.329 1 52.87 ? N7 P0V 301 C 1 HETATM 33 O O11 P0V . . . G 2 -11.807 -25.769 21.506 1 44.79 ? O11 P0V 301 C 1 HETATM 34 O O22 P0V . . . G 2 -12.972 -25.608 24.746 1 53.55 ? O22 P0V 301 C 1 HETATM 35 O O23 P0V . . . G 2 -10.911 -24.082 24.558 1 53.56 ? O23 P0V 301 C 1 HETATM 36 O O35 P0V . . . G 2 -21.042 -26.742 15.851 1 43.13 ? O35 P0V 301 C 1 HETATM 37 O O37 P0V . . . G 2 -14.332 -33.721 22.559 1 47.06 ? O37 P0V 301 C 1 HETATM 38 O O38 P0V . . . G 2 -16.093 -32.583 22.491 1 38.84 ? O38 P0V 301 C 1 HETATM 39 H H281 P0V . . . G 2 -18.463 -26.903 18.486 1 47.89 ? H281 P0V 301 C 1 HETATM 40 H H301 P0V . . . G 2 -21.716 -28.975 17.329 1 53.17 ? H301 P0V 301 C 1 HETATM 41 H H192 P0V . . . G 2 -15.042 -30.104 21.738 1 49.79 ? H192 P0V 301 C 1 HETATM 42 H H191 P0V . . . G 2 -15.721 -30.221 23.108 1 49.79 ? H191 P0V 301 C 1 HETATM 43 H H141 P0V . . . G 2 -10.084 -25.587 23.607 1 59.15 ? H141 P0V 301 C 1 HETATM 44 H H152 P0V . . . G 2 -14.111 -25.901 21.608 1 58.74 ? H152 P0V 301 C 1 HETATM 45 H H151 P0V . . . G 2 -14.269 -25.892 23.133 1 58.74 ? H151 P0V 301 C 1 HETATM 46 H H131 P0V . . . G 2 -11.624 -26.927 24.302 1 56.87 ? H131 P0V 301 C 1 HETATM 47 H H121 P0V . . . G 2 -12.312 -27.534 22.47 1 56.02 ? H121 P0V 301 C 1 HETATM 48 H H41 P0V . . . G 2 -6.48 -25.717 22.262 1 60.9 ? H41 P0V 301 C 1 HETATM 49 H H81 P0V . . . G 2 -11.561 -22.435 21.106 1 65.71 ? H81 P0V 301 C 1 HETATM 50 H H101 P0V . . . G 2 -11.929 -23.872 22.508 1 58.87 ? H101 P0V 301 C 1 HETATM 51 H H182 P0V . . . G 2 -14.393 -28.654 24.026 1 53.06 ? H182 P0V 301 C 1 HETATM 52 H H181 P0V . . . G 2 -13.301 -28.85 22.968 1 53.06 ? H181 P0V 301 C 1 HETATM 53 H H201 P0V . . . G 2 -13.208 -31.268 22.511 1 52.23 ? H201 P0V 301 C 1 HETATM 54 H H242 P0V . . . G 2 -16.326 -27.893 23.614 1 54.55 ? H242 P0V 301 C 1 HETATM 55 H H241 P0V . . . G 2 -16.219 -26.451 23.102 1 54.55 ? H241 P0V 301 C 1 HETATM 56 H H311 P0V . . . G 2 -21.753 -30.06 19.386 1 52.31 ? H311 P0V 301 C 1 HETATM 57 H H321 P0V . . . G 2 -20.131 -29.572 20.987 1 52.2 ? H321 P0V 301 C 1 HETATM 58 H H172 P0V . . . G 2 -6.211 -21.559 19.901 1 59.64 ? H172 P0V 301 C 1 HETATM 59 H H171 P0V . . . G 2 -6.697 -22.35 18.718 1 59.64 ? H171 P0V 301 C 1 HETATM 60 H H212 P0V . . . G 2 -14.23 -31.019 24.908 1 55.94 ? H212 P0V 301 C 1 HETATM 61 H H341 P0V . . . G 2 -18.035 -27.416 15.883 1 56.59 ? H341 P0V 301 C 1 HETATM 62 H H342 P0V . . . G 2 -18.754 -26.695 14.776 1 56.59 ? H342 P0V 301 C 1 HETATM 63 H H221 P0V . . . G 2 -13.232 -26.206 25.269 1 64.38 ? H221 P0V 301 C 1 HETATM 64 H H231 P0V . . . G 2 -11.674 -23.943 24.837 1 64.39 ? H231 P0V 301 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 204 _model_server_stats.query_time_ms 1701 _model_server_stats.encode_time_ms 123 _model_server_stats.element_count 64 #