0.017886 0.010326 0.000000 0.000000 0.020653 0.000000 0.000000 0.000000 0.008571 0.00000 0.00000 0.00000 Gunther, Z. Papke, B. Ismail, S. Vartak, N. Chandra, A. Hoffmann, M. Hahn, S. Triola, G. Wittinghofer, A. Bastiaens, P. Waldmann, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 55.910 55.910 116.670 C40 H42 N6 O2 638.800 (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Y 1 N C Y 2 N C Y 3 N C Y 4 N C Y 5 N C Y 6 N C N 7 N C Y 8 N N Y 9 N C Y 10 N C Y 11 N C Y 12 N C Y 13 N C Y 14 N C Y 15 N N Y 16 N C N 17 N N N 18 N C N 19 N C N 20 N C N 21 N C N 22 N C N 23 N C N 24 N O N 25 N O N 26 N C N 27 S C N 28 N C N 29 N C N 30 N C N 31 N N N 32 N C N 33 N C Y 34 N N Y 35 N C Y 36 N C Y 37 N C Y 38 N C Y 39 N C Y 40 N C Y 41 N N Y 42 N C Y 43 N C Y 44 N C Y 45 N C Y 46 N C Y 47 N C Y 48 N C N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N N N 92 S C N 93 N C N 94 N O N 95 N C N 96 N O N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N N N 105 S C N 106 N C N 107 N O N 108 N C N 109 N C N 110 N C N 111 N N N 112 N C N 113 N N N 114 N N N 115 N O N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N C N 137 N O N 138 N N N 139 N O N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N N N 149 S C N 150 N C N 151 N O N 152 N C N 153 N C N 154 N O N 155 N O N 156 N O N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N N N 165 R C N 166 N C N 167 N O N 168 N C N 169 N S N 170 N O N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N N N 179 S C N 180 N C N 181 N O N 182 N C N 183 N C N 184 N C N 185 N O N 186 N N N 187 N O N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N N N 199 S C N 200 N C N 201 N O N 202 N C N 203 N C N 204 N C N 205 N O N 206 N O N 207 N O N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N N N 218 N C N 219 N C N 220 N O N 221 N O N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N N N 228 S C N 229 N C N 230 N O N 231 N C Y 232 N C Y 233 N N Y 234 N C Y 235 N C Y 236 N N N 237 N O N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N O N 249 N H N 250 N H N 251 N N N 252 S C N 253 N C N 254 N O N 255 S C N 256 N C N 257 N C N 258 N C N 259 N O N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N N N 274 S C N 275 N C N 276 N O N 277 N C N 278 N C N 279 N C N 280 N C N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N N N 296 S C N 297 N C N 298 N O N 299 N C N 300 N C N 301 N C N 302 N C N 303 N N N 304 N O N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N N N 321 S C N 322 N C N 323 N O N 324 N C N 325 N C N 326 N S N 327 N C N 328 N O N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N N N 341 S C N 342 N C N 343 N O N 344 N C Y 345 N C Y 346 N C Y 347 N C Y 348 N C Y 349 N C Y 350 N C N 351 N O N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N N N 364 S C N 365 N C N 366 N O N 367 N C N 368 N C N 369 N C N 370 N O N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N N N 381 S C N 382 N C N 383 N O N 384 N C N 385 N O N 386 N O N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N N N 395 S C N 396 N C N 397 N O N 398 R C N 399 N O N 400 N C N 401 N O N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N N N 412 S C N 413 N C N 414 N O N 415 N C Y 416 N C Y 417 N C Y 418 N C Y 419 N N Y 420 N C Y 421 N C Y 422 N C Y 423 N C Y 424 N C N 425 N O N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N N N 439 S C N 440 N C N 441 N O N 442 N C Y 443 N C Y 444 N C Y 445 N C Y 446 N C Y 447 N C Y 448 N C N 449 N O N 450 N O N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N N N 463 S C N 464 N C N 465 N O N 466 N C N 467 N C N 468 N C N 469 N O N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H Y 1 N doub Y 2 N sing Y 3 N sing Y 4 N sing Y 5 N doub Y 6 N doub N 7 N sing N 8 N sing Y 9 N doub N 10 N sing N 11 N sing Y 12 N sing N 13 N sing N 14 N sing N 15 N sing Y 16 N sing Y 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing Y 33 N doub Y 34 N sing Y 35 N doub Y 36 N sing Y 37 N sing Y 38 N sing Y 39 N doub Y 40 N sing Y 41 N sing Y 42 N doub Y 43 N doub Y 44 N doub Y 45 N sing Y 46 N sing Y 47 N sing N 48 N sing Y 49 N doub Y 50 N doub Y 51 N sing Y 52 N sing Y 53 N doub Y 54 N doub Y 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N doub N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N doub N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N doub N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N doub N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N doub N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N doub N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N doub N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N doub N 233 N sing N 234 N sing N 235 N sing N 236 N sing Y 237 N sing Y 238 N doub Y 239 N doub N 240 N sing Y 241 N sing N 242 N sing Y 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N doub N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N doub N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N doub N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N doub N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N doub N 341 N sing N 342 N sing N 343 N sing N 344 N sing Y 345 N doub Y 346 N sing Y 347 N sing N 348 N sing Y 349 N doub N 350 N sing Y 351 N doub N 352 N sing Y 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N doub N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N doub N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N doub N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N doub N 410 N sing N 411 N sing N 412 N sing N 413 N sing Y 414 N doub Y 415 N sing Y 416 N sing N 417 N sing Y 418 N doub Y 419 N sing Y 420 N sing N 421 N sing Y 422 N sing Y 423 N doub N 424 N sing Y 425 N doub N 426 N sing Y 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N doub N 438 N sing N 439 N sing N 440 N sing N 441 N sing Y 442 N doub Y 443 N sing Y 444 N sing N 445 N sing Y 446 N doub N 447 N sing Y 448 N doub N 449 N sing Y 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N doub N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing UK Nature NATUAS 0006 0028-0836 497 638 642 10.1038/nature12205 23698361 Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling 2013 10.2210/pdb4jvf/pdb pdb_00004jvf 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 PIXEL 2012-03-01 DECTRIS PILATUS 6M SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 1 1.0 X10SA SLS 1 SYNCHROTRON SLS BEAMLINE X10SA 17585.121 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta 1 man polymer 638.800 (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate 1 syn non-polymer 18.015 water 47 nat water GMP-PDE delta, Protein p17 no no GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample PDE6D, PDED 9606 Homo sapiens 562 Escherichia coli 1 2.99 58.91 VAPOR DIFFUSION, SITTING DROP 7.4 18% PEG 4000, 25mM Sodium Acetate, 200mM Ammonium Sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Database references Refinement description Data collection Database references Derived calculations Refinement description 1 0 2013-05-22 1 1 2013-06-05 1 2 2017-11-15 1 3 2023-09-20 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2013-03-25 REL REL 17X (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate HOH water 3T5G PDB experimental model DRG 1 2 17X 17X 201 B HOH 4 3 HOH HOH 301 B HOH 6 3 HOH HOH 302 B HOH 7 3 HOH HOH 303 B HOH 8 3 HOH HOH 304 B HOH 9 3 HOH HOH 305 B HOH 11 3 HOH HOH 306 B HOH 12 3 HOH HOH 307 B HOH 13 3 HOH HOH 308 B HOH 14 3 HOH HOH 309 B HOH 15 3 HOH HOH 310 B HOH 16 3 HOH HOH 311 B HOH 17 3 HOH HOH 312 B HOH 18 3 HOH HOH 313 B HOH 19 3 HOH HOH 314 B HOH 20 3 HOH HOH 315 B HOH 22 3 HOH HOH 316 B HOH 23 3 HOH HOH 317 B HOH 24 3 HOH HOH 318 B HOH 25 3 HOH HOH 319 B HOH 26 3 HOH HOH 320 B HOH 27 3 HOH HOH 321 B HOH 28 3 HOH HOH 322 B HOH 29 3 HOH HOH 323 B HOH 30 3 HOH HOH 324 B HOH 31 3 HOH HOH 325 B HOH 32 3 HOH HOH 326 B HOH 34 3 HOH HOH 327 B HOH 36 3 HOH HOH 328 B HOH 38 3 HOH HOH 329 B HOH 39 3 HOH HOH 330 B HOH 40 3 HOH HOH 331 B HOH 41 3 HOH HOH 332 B HOH 43 3 HOH HOH 333 B HOH 46 3 HOH HOH 334 B HOH 47 3 HOH HOH 335 B HOH 49 3 HOH HOH 336 B HOH 50 3 HOH HOH 337 B HOH 52 3 HOH HOH 338 B HOH 53 3 HOH HOH 339 B HOH 54 3 HOH HOH 340 B HOH 55 3 HOH HOH 341 B HOH 57 3 HOH HOH 342 B HOH 58 3 HOH HOH 343 B HOH 61 3 HOH HOH 344 B HOH 62 3 HOH HOH 345 B HOH 63 3 HOH HOH 346 B HOH 64 3 HOH HOH 347 B n 1 -1 B n 2 0 B n 3 1 B n 4 2 B n 5 3 B LYS 4 n 6 LYS 4 B ASP 5 n 7 ASP 5 B GLU 6 n 8 GLU 6 B ARG 7 n 9 ARG 7 B ALA 8 n 10 ALA 8 B ARG 9 n 11 ARG 9 B GLU 10 n 12 GLU 10 B ILE 11 n 13 ILE 11 B LEU 12 n 14 LEU 12 B ARG 13 n 15 ARG 13 B GLY 14 n 16 GLY 14 B PHE 15 n 17 PHE 15 B LYS 16 n 18 LYS 16 B LEU 17 n 19 LEU 17 B ASN 18 n 20 ASN 18 B TRP 19 n 21 TRP 19 B MET 20 n 22 MET 20 B ASN 21 n 23 ASN 21 B LEU 22 n 24 LEU 22 B ARG 23 n 25 ARG 23 B ASP 24 n 26 ASP 24 B ALA 25 n 27 ALA 25 B ALA 26 n 28 GLU 26 B THR 27 n 29 THR 27 B GLY 28 n 30 GLY 28 B LYS 29 n 31 LYS 29 B ILE 30 n 32 ILE 30 B LEU 31 n 33 LEU 31 B TRP 32 n 34 TRP 32 B GLN 33 n 35 GLN 33 B GLY 34 n 36 GLY 34 B THR 35 n 37 THR 35 B GLU 36 n 38 GLU 36 B ASP 37 n 39 ASP 37 B LEU 38 n 40 LEU 38 B SER 39 n 41 SER 39 B VAL 40 n 42 VAL 40 B PRO 41 n 43 PRO 41 B GLY 42 n 44 GLY 42 B VAL 43 n 45 VAL 43 B GLU 44 n 46 GLU 44 B HIS 45 n 47 HIS 45 B GLU 46 n 48 GLU 46 B ALA 47 n 49 ALA 47 B ARG 48 n 50 ARG 48 B VAL 49 n 51 VAL 49 B PRO 50 n 52 PRO 50 B LYS 51 n 53 LYS 51 B LYS 52 n 54 LYS 52 B ILE 53 n 55 ILE 53 B LEU 54 n 56 LEU 54 B LYS 55 n 57 LYS 55 B CYS 56 n 58 CYS 56 B LYS 57 n 59 LYS 57 B ALA 58 n 60 ALA 58 B VAL 59 n 61 VAL 59 B SER 60 n 62 SER 60 B ARG 61 n 63 ARG 61 B GLU 62 n 64 GLU 62 B LEU 63 n 65 LEU 63 B ASN 64 n 66 ASN 64 B PHE 65 n 67 PHE 65 B SER 66 n 68 SER 66 B SER 67 n 69 SER 67 B THR 68 n 70 THR 68 B GLU 69 n 71 GLU 69 B GLN 70 n 72 GLN 70 B MET 71 n 73 MET 71 B GLU 72 n 74 GLU 72 B LYS 73 n 75 LYS 73 B PHE 74 n 76 PHE 74 B ARG 75 n 77 ARG 75 B LEU 76 n 78 LEU 76 B GLU 77 n 79 GLU 77 B GLN 78 n 80 GLN 78 B LYS 79 n 81 LYS 79 B VAL 80 n 82 VAL 80 B TYR 81 n 83 TYR 81 B PHE 82 n 84 PHE 82 B LYS 83 n 85 LYS 83 B GLY 84 n 86 GLY 84 B GLN 85 n 87 GLN 85 B CYS 86 n 88 CYS 86 B LEU 87 n 89 LEU 87 B GLU 88 n 90 GLU 88 B GLU 89 n 91 GLU 89 B TRP 90 n 92 TRP 90 B PHE 91 n 93 PHE 91 B PHE 92 n 94 PHE 92 B GLU 93 n 95 GLU 93 B PHE 94 n 96 PHE 94 B GLY 95 n 97 GLY 95 B PHE 96 n 98 PHE 96 B VAL 97 n 99 VAL 97 B ILE 98 n 100 ILE 98 B PRO 99 n 101 PRO 99 B ASN 100 n 102 ASN 100 B SER 101 n 103 SER 101 B THR 102 n 104 THR 102 B ASN 103 n 105 ASN 103 B THR 104 n 106 THR 104 B TRP 105 n 107 TRP 105 B GLN 106 n 108 GLN 106 B SER 107 n 109 SER 107 B LEU 108 n 110 LEU 108 B ILE 109 n 111 ILE 109 B GLU 110 n 112 GLU 110 B ALA 111 n 113 ALA 111 B n 114 112 B n 115 113 B n 116 114 B n 117 115 B n 118 116 B n 119 117 B MET 118 n 120 MET 118 B PRO 119 n 121 PRO 119 B ALA 120 n 122 ALA 120 B SER 121 n 123 SER 121 B VAL 122 n 124 VAL 122 B LEU 123 n 125 LEU 123 B THR 124 n 126 THR 124 B GLY 125 n 127 GLY 125 B ASN 126 n 128 ASN 126 B VAL 127 n 129 VAL 127 B ILE 128 n 130 ILE 128 B ILE 129 n 131 ILE 129 B GLU 130 n 132 GLU 130 B THR 131 n 133 THR 131 B LYS 132 n 134 LYS 132 B PHE 133 n 135 PHE 133 B PHE 134 n 136 PHE 134 B ASP 135 n 137 ASP 135 B ASP 136 n 138 ASP 136 B ASP 137 n 139 ASP 137 B LEU 138 n 140 LEU 138 B LEU 139 n 141 LEU 139 B VAL 140 n 142 VAL 140 B SER 141 n 143 SER 141 B THR 142 n 144 THR 142 B SER 143 n 145 SER 143 B ARG 144 n 146 ARG 144 B VAL 145 n 147 VAL 145 B ARG 146 n 148 ARG 146 B LEU 147 n 149 LEU 147 B PHE 148 n 150 PHE 148 B TYR 149 n 151 TYR 149 B VAL 150 n 152 VAL 150 B author_and_software_defined_assembly PISA 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 B O TRP 32 A O TRP 34 B N LEU 22 A N LEU 24 B N ARG 23 A N ARG 25 B O SER 60 A O SER 62 B N ARG 61 A N ARG 63 B O SER 107 A O SER 109 B N HIS 45 A N HIS 47 B O ARG 146 A O ARG 148 B O VAL 140 A O VAL 142 B N PHE 133 A N PHE 135 B O ILE 128 A O ILE 130 B N TYR 81 A N TYR 83 B N VAL 80 A N VAL 82 B O LEU 87 A O LEU 89 1 B CG GLU 26 A CG GLU 28 1 Y 1 B CD GLU 26 A CD GLU 28 1 Y 1 B OE1 GLU 26 A OE1 GLU 28 1 Y 1 B OE2 GLU 26 A OE2 GLU 28 1 Y 1 B GLY -1 A GLY 1 1 Y 1 B SER 0 A SER 2 1 Y 1 B MET 1 A MET 3 1 Y 1 B SER 2 A SER 4 1 Y 1 B ALA 3 A ALA 5 1 Y 1 B ALA 112 A ALA 114 1 Y 1 B PRO 113 A PRO 115 1 Y 1 B GLU 114 A GLU 116 1 Y 1 B SER 115 A SER 117 1 Y 1 B GLN 116 A GLN 118 1 Y 1 B MET 117 A MET 119 1 Y 1 B B NE O ARG HOH 144 325 2.18 1 B B PHE ASP 134 135 147.48 1 -14.07 2.10 111.80 97.73 B B B CG CD NE ARG ARG ARG 13 13 13 N 1 B ASP 136 52.39 -114.44 31.222 1.46 0.73 0.00 1.46 0.00 -2.20 0.936 0.906 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 0.25659 0.20697 0.20949 2.40 27.9 433 8225 8225 5.0 99.04 7.480 0.174 RANDOM 1 THROUGHOUT -3 0.317 0.245 0.80 0.80 1.20 3T5G MAXIMUM LIKELIHOOD MASK 2.40 27.9 47 1253 48 0 1158 0.022 0.022 1237 1.980 2.001 1668 7.743 5.000 139 41.363 23.793 58 18.107 15.000 220 17.629 15.000 9 0.123 0.200 177 0.009 0.021 924 0.409 0.250 2.462 27 520 20 98.56 2.4 27.9 4JVF 8659 8659 -3 -3 0.122 1 99 2.4 2.5 1 98.8 data collection ProDC phasing MOLREP refinement REFMAC 5.6.0093 data reduction XDS data scaling XSCALE The Crystal structure of PDE6D in complex with the inhibitor (s)-5 1 N N 2 N N 3 N N B LYS 4 A LYS 6 HELX_P B GLY 14 A GLY 16 1 1 11 B LYS 52 A LYS 54 HELX_P B LYS 55 A LYS 57 5 2 4 B PRO 119 A PRO 121 HELX_P B THR 124 A THR 126 1 3 6 Protein binding/inhibitor Immunoglobulin-like beta-sandwich, GDI-like solubilizing factor, Prenyl binding, Protein binding-inhibitor complex PDE6D_HUMAN UNP 1 1 O43924 MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKV YFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 1 150 4JVF 1 150 O43924 B 1 3 152 1 expression tag GLY -1 4JVF B O43924 UNP 1 1 expression tag SER 0 4JVF B O43924 UNP 2 4 5 anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel B ILE 30 A ILE 32 B GLY 34 A GLY 36 B PHE 15 A PHE 17 B ASP 24 A ASP 26 B ALA 58 A ALA 60 B SER 67 A SER 69 B SER 101 A SER 103 B GLU 110 A GLU 112 B GLU 44 A GLU 46 B PRO 50 A PRO 52 B LEU 138 A LEU 140 B VAL 150 A VAL 152 B VAL 127 A VAL 129 B ASP 135 A ASP 137 B MET 71 A MET 73 B PHE 82 A PHE 84 B GLN 85 A GLN 87 B VAL 97 A VAL 99 BINDING SITE FOR RESIDUE 17X B 201 B 17X 201 Software 14 B LEU 38 A LEU 40 14 1_555 B ALA 47 A ALA 49 14 1_555 B ILE 53 A ILE 55 14 1_555 B LEU 54 A LEU 56 14 1_555 B CYS 56 A CYS 58 14 1_555 B LYS 57 A LYS 59 14 1_555 B ARG 61 A ARG 63 14 1_555 B GLN 78 A GLN 80 14 1_555 B VAL 80 A VAL 82 14 1_555 B TRP 90 A TRP 92 14 1_555 B ILE 109 A ILE 111 14 1_555 B ILE 129 A ILE 131 14 1_555 B LEU 147 A LEU 149 14 1_555 B TYR 149 A TYR 151 14 1_555 154 P 32 2 1