data_6PVS # _model_server_result.job_id QBzNu5HZZQfpDMfbV5yDjg _model_server_result.datetime_utc '2025-02-20 11:47:42' _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":"F","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 . . . F 2 -15.881 -23.643 -17.885 1 37.86 ? C28 P0V 301 B 1 HETATM 2 C C29 P0V . . . F 2 -14.94 -24.7 -17.917 1 41.28 ? C29 P0V 301 B 1 HETATM 3 C C30 P0V . . . F 2 -13.769 -24.563 -18.642 1 42.27 ? C30 P0V 301 B 1 HETATM 4 C C27 P0V . . . F 2 -15.598 -22.436 -18.515 1 36.04 ? C27 P0V 301 B 1 HETATM 5 C C26 P0V . . . F 2 -16.611 -21.277 -18.432 1 39.29 ? C26 P0V 301 B 1 HETATM 6 C C19 P0V . . . F 2 -19.491 -19.609 -21.162 1 34.75 ? C19 P0V 301 B 1 HETATM 7 C C14 P0V . . . F 2 -23.475 -17.736 -16.254 1 38.58 ? C14 P0V 301 B 1 HETATM 8 C C15 P0V . . . F 2 -20.688 -19.386 -17.462 1 34.13 ? C15 P0V 301 B 1 HETATM 9 C C13 P0V . . . F 2 -22.509 -17.75 -17.363 1 41.72 ? C13 P0V 301 B 1 HETATM 10 C C12 P0V . . . F 2 -22.147 -19.155 -17.69 1 36.78 ? C12 P0V 301 B 1 HETATM 11 C C6 P0V . . . F 2 -27.377 -20.662 -14.151 1 37.54 ? C6 P0V 301 B 1 HETATM 12 C C4 P0V . . . F 2 -27.316 -20.062 -16.42 1 37.96 ? C4 P0V 301 B 1 HETATM 13 N N3 P0V . . . F 2 -26.048 -19.674 -16.34 1 38.59 ? N3 P0V 301 B 1 HETATM 14 C C2 P0V . . . F 2 -25.402 -19.766 -15.172 1 38.95 ? C2 P0V 301 B 1 HETATM 15 C C1 P0V . . . F 2 -26.058 -20.275 -14.023 1 38.17 ? C1 P0V 301 B 1 HETATM 16 N N9 P0V . . . F 2 -24.3 -19.512 -14.729 1 40.09 ? N9 P0V 301 B 1 HETATM 17 C C8 P0V . . . F 2 -23.975 -19.722 -13.563 1 38.48 ? C8 P0V 301 B 1 HETATM 18 C C10 P0V . . . F 2 -23.293 -19.018 -15.579 1 37 ? C10 P0V 301 B 1 HETATM 19 C C18 P0V . . . F 2 -20.23 -18.888 -19.974 1 29.33 ? C18 P0V 301 B 1 HETATM 20 C C20 P0V . . . F 2 -19.964 -19.532 -22.621 1 35.65 ? C20 P0V 301 B 1 HETATM 21 C C24 P0V . . . F 2 -18.446 -19.198 -18.275 1 35.68 ? C24 P0V 301 B 1 HETATM 22 C C25 P0V . . . F 2 -17.418 -20.371 -18.359 1 38.9 ? C25 P0V 301 B 1 HETATM 23 C C31 P0V . . . F 2 -13.489 -23.353 -19.291 1 40.01 ? C31 P0V 301 B 1 HETATM 24 C C32 P0V . . . F 2 -14.406 -22.294 -19.223 1 40.29 ? C32 P0V 301 B 1 HETATM 25 C C33 P0V . . . F 2 -15.231 -26.039 -17.216 1 36.22 ? C33 P0V 301 B 1 HETATM 26 C C36 P0V . . . F 2 -18.623 -19.244 -23.456 1 37.64 ? C36 P0V 301 B 1 HETATM 27 N N16 P0V . . . F 2 -19.834 -19.616 -18.69 1 32.19 ? N16 P0V 301 B 1 HETATM 28 N N17 P0V . . . F 2 -28.094 -21.207 -13.015 1 36.7 ? N17 P0V 301 B 1 HETATM 29 N N21 P0V . . . F 2 -21.063 -18.593 -22.842 1 35.14 ? N21 P0V 301 B 1 HETATM 30 N N34 P0V . . . F 2 -16.22 -26.992 -17.718 1 39.13 ? N34 P0V 301 B 1 HETATM 31 N N5 P0V . . . F 2 -27.964 -20.547 -15.349 1 37.44 ? N5 P0V 301 B 1 HETATM 32 N N7 P0V . . . F 2 -25.056 -20.218 -12.989 1 36.96 ? N7 P0V 301 B 1 HETATM 33 O O11 P0V . . . F 2 -22.989 -19.989 -16.756 1 34.3 ? O11 P0V 301 B 1 HETATM 34 O O22 P0V . . . F 2 -21.393 -16.935 -16.912 1 34.99 ? O22 P0V 301 B 1 HETATM 35 O O23 P0V . . . F 2 -23.147 -16.804 -15.201 1 38.03 ? O23 P0V 301 B 1 HETATM 36 O O35 P0V . . . F 2 -14.698 -26.244 -16.158 1 34.33 ? O35 P0V 301 B 1 HETATM 37 O O37 P0V . . . F 2 -18.367 -19.925 -24.47 1 37.17 ? O37 P0V 301 B 1 HETATM 38 O O38 P0V . . . F 2 -17.647 -18.447 -23.195 1 38.2 ? O38 P0V 301 B 1 HETATM 39 H H281 P0V . . . F 2 -16.689 -23.756 -17.442 1 45.56 ? H281 P0V 301 B 1 HETATM 40 H H301 P0V . . . F 2 -13.17 -25.271 -18.697 1 50.84 ? H301 P0V 301 B 1 HETATM 41 H H192 P0V . . . F 2 -19.481 -20.522 -20.943 1 41.82 ? H192 P0V 301 B 1 HETATM 42 H H191 P0V . . . F 2 -18.613 -19.277 -21.158 1 41.82 ? H191 P0V 301 B 1 HETATM 43 H H141 P0V . . . F 2 -24.315 -17.547 -16.628 1 46.42 ? H141 P0V 301 B 1 HETATM 44 H H152 P0V . . . F 2 -20.604 -20.142 -16.911 1 41.08 ? H152 P0V 301 B 1 HETATM 45 H H151 P0V . . . F 2 -20.348 -18.634 -17.015 1 41.08 ? H151 P0V 301 B 1 HETATM 46 H H131 P0V . . . F 2 -22.859 -17.408 -18.164 1 50.19 ? H131 P0V 301 B 1 HETATM 47 H H121 P0V . . . F 2 -22.319 -19.366 -18.589 1 44.26 ? H121 P0V 301 B 1 HETATM 48 H H41 P0V . . . F 2 -27.762 -19.997 -17.232 1 45.68 ? H41 P0V 301 B 1 HETATM 49 H H81 P0V . . . F 2 -23.261 -19.327 -13.121 1 46.3 ? H81 P0V 301 B 1 HETATM 50 H H101 P0V . . . F 2 -22.603 -18.909 -14.951 1 44.52 ? H101 P0V 301 B 1 HETATM 51 H H182 P0V . . . F 2 -19.966 -17.988 -19.93 1 35.32 ? H182 P0V 301 B 1 HETATM 52 H H181 P0V . . . F 2 -21.16 -18.936 -20.098 1 35.32 ? H181 P0V 301 B 1 HETATM 53 H H201 P0V . . . F 2 -20.368 -20.328 -22.909 1 42.91 ? H201 P0V 301 B 1 HETATM 54 H H242 P0V . . . F 2 -18.158 -18.505 -18.84 1 42.94 ? H242 P0V 301 B 1 HETATM 55 H H241 P0V . . . F 2 -18.476 -18.888 -17.389 1 42.94 ? H241 P0V 301 B 1 HETATM 56 H H311 P0V . . . F 2 -12.697 -23.253 -19.766 1 48.13 ? H311 P0V 301 B 1 HETATM 57 H H321 P0V . . . F 2 -14.217 -21.492 -19.653 1 48.47 ? H321 P0V 301 B 1 HETATM 58 H H172 P0V . . . F 2 -28.305 -20.71 -12.339 1 44.16 ? H172 P0V 301 B 1 HETATM 59 H H171 P0V . . . F 2 -28.294 -22.054 -13.015 1 44.16 ? H171 P0V 301 B 1 HETATM 60 H H212 P0V . . . F 2 -21.432 -18.629 -23.644 1 42.3 ? H212 P0V 301 B 1 HETATM 61 H H341 P0V . . . F 2 -16.353 -27.732 -17.288 1 47.08 ? H341 P0V 301 B 1 HETATM 62 H H342 P0V . . . F 2 -16.608 -26.848 -18.476 1 47.08 ? H342 P0V 301 B 1 HETATM 63 H H221 P0V . . . F 2 -20.939 -16.707 -17.569 1 42.11 ? H221 P0V 301 B 1 HETATM 64 H H231 P0V . . . F 2 -23.037 -16.062 -15.541 1 45.76 ? H231 P0V 301 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 64 #