0.009897 0.000000 0.007485 0.000000 0.017629 0.000000 0.000000 0.000000 0.016879 0.00000 0.00000 0.00000 Yeoh, S. Innocenti, P. Hoelder, S. Bayliss, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 127.10 90.00 101.039 56.724 74.279 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 C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer C24 H25 F3 N4 O2 S 490.541 4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{[(1R,2Z)-4,4,4-TRIFLUORO-1-METHYLBUT-2-EN-1-YL]OXY}BENZAMIDE non-polymer 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 N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O 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 N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O 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 N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O 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 C N 89 N O N 90 N C N 91 N O N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N C N 99 R C N 100 N C N 101 N C N 102 N C N 103 N F N 104 N F N 105 N F N 106 N O Y 107 N C Y 108 N C Y 109 N C Y 110 N C Y 111 N C Y 112 N C Y 113 N C Y 114 N C Y 115 N C N 116 N C N 117 N N N 118 N C N 119 N C Y 120 N C Y 121 N S Y 122 N C Y 123 N N Y 124 N C N 125 N N Y 126 N C Y 127 N C Y 128 N C N 129 N C N 130 N N N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H 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 H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N N N 158 S C N 159 N C N 160 N O N 161 N C N 162 N C N 163 N C N 164 N O N 165 N N N 166 N O N 167 N H N 168 N H N 169 N H N 170 N H 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 N N 178 S C N 179 N C N 180 N O N 181 N C N 182 N C N 183 N C N 184 N O N 185 N O N 186 N O N 187 N H 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 N N 197 N C N 198 N C N 199 N O N 200 N O N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N N N 207 S C N 208 N C N 209 N O N 210 N C Y 211 N C Y 212 N N Y 213 N C Y 214 N C Y 215 N N N 216 N O N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N O N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 S C N 235 N C N 236 N C N 237 N C N 238 N O 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 H N 249 N H N 250 N H N 251 N H N 252 N N N 253 S C N 254 N C N 255 N O N 256 N C N 257 N C N 258 N C N 259 N C N 260 N O 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 H N 274 N N N 275 S C N 276 N C N 277 N O N 278 N C N 279 N C N 280 N C N 281 N C N 282 N N N 283 N O 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 H N 296 N H N 297 N H N 298 N H N 299 N N N 300 S C N 301 N C N 302 N O N 303 N C N 304 N C N 305 N S N 306 N C N 307 N O 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 N N 320 S C N 321 N C N 322 N O N 323 N C Y 324 N C Y 325 N C Y 326 N C Y 327 N C Y 328 N C Y 329 N C N 330 N O 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 H N 341 N H N 342 N N N 343 S C N 344 N C N 345 N O N 346 N C N 347 N C N 348 N C N 349 N O N 350 N H N 351 N H 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 N N 360 S C N 361 N C N 362 N O N 363 N C N 364 N O N 365 N O N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N N N 374 S C N 375 N C N 376 N O N 377 R C N 378 N O N 379 N C N 380 N O N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N N N 391 S C N 392 N C N 393 N O N 394 N C Y 395 N C Y 396 N C Y 397 N C Y 398 N N Y 399 N C Y 400 N C Y 401 N C Y 402 N C Y 403 N C N 404 N O 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 H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N N N 418 S C N 419 N C N 420 N O N 421 N C Y 422 N C Y 423 N C Y 424 N C Y 425 N C Y 426 N C Y 427 N C N 428 N O N 429 N O 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 H N 439 N H N 440 N H N 441 N N N 442 S C N 443 N C N 444 N O N 445 N C N 446 N C N 447 N C N 448 N O N 449 N H N 450 N H 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 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub 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 sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 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 doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub 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 doub 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 Z doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing Y 101 N sing Y 102 N doub Y 103 N doub N 104 N sing Y 105 N sing Y 106 N doub Y 107 N sing Y 108 N sing N 109 N sing Y 110 N doub Y 111 N doub Y 112 N sing Y 113 N sing N 114 N sing Y 115 N doub N 116 N sing N 117 N sing N 118 N sing Y 119 N sing Y 120 N sing Y 121 N doub N 122 N sing Y 123 N doub Y 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing 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 sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing 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 sing N 159 N doub N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N doub N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N doub 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 sing N 195 N sing N 196 N doub 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 Y 210 N sing Y 211 N doub Y 212 N doub N 213 N sing Y 214 N sing N 215 N sing Y 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 sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N doub N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 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 doub N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing 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 doub N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing 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 doub N 295 N sing N 296 N sing N 297 N sing 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 doub N 314 N sing N 315 N sing N 316 N sing N 317 N sing Y 318 N doub Y 319 N sing Y 320 N sing N 321 N sing Y 322 N doub N 323 N sing Y 324 N doub N 325 N sing Y 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 doub N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N doub 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 sing N 364 N sing N 365 N sing N 366 N doub 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 sing N 381 N sing N 382 N doub N 383 N sing N 384 N sing N 385 N sing N 386 N sing Y 387 N doub Y 388 N sing Y 389 N sing N 390 N sing Y 391 N doub Y 392 N sing Y 393 N sing N 394 N sing Y 395 N sing Y 396 N doub N 397 N sing Y 398 N doub N 399 N sing Y 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 sing N 410 N doub N 411 N sing N 412 N sing N 413 N sing N 414 N sing Y 415 N doub Y 416 N sing Y 417 N sing N 418 N sing Y 419 N doub N 420 N sing Y 421 N doub N 422 N sing Y 423 N sing N 424 N sing N 425 N sing N 426 N sing N 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 doub N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing US J.Med.Chem. JMCMAR 0151 0022-2623 55 3228 10.1021/JM201683B 22404346 Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase Nek2: Structure-Activity Relationship, Structural Biology, and Cellular Activity. 2012 10.2210/pdb4afe/pdb pdb_00004afe 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 CCD 2011-12-12 ADSC CCD SINGLE WAVELENGTH M x-ray 1 0.96860 1.0 I24 Diamond 0.96860 SYNCHROTRON DIAMOND BEAMLINE I24 32662.479 SERINE/THREONINE-PROTEIN KINASE NEK2 2.7.11.1 CATALYTIC DOMAIN, RESIDUES 1-271 1 man polymer 490.541 4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{[(1R,2Z)-4,4,4-TRIFLUORO-1-METHYLBUT-2-EN-1-YL]OXY}BENZAMIDE 1 syn non-polymer 62.068 1,2-ETHANEDIOL 1 syn non-polymer 18.015 water 32 nat water HSPK 21, NEVER IN MITOSIS A-RELATED KINASE 2, NIMA-RELATED PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, NEK2 no no MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT TLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDF GLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT TLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDF GLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH A 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 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 9606 HOMO SAPIENS 469008 ESCHERICHIA COLI BL21(DE3) CODONPLUS RIL PLASMID PET30 1 2.61 52.85 NONE chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_initial_refinement_model struct_site repository Initial release Data collection Database references Derived calculations Other Refinement description 1 0 2012-04-25 1 1 2023-12-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 14 HUMAN NEK2 KINASE ATPGAMMAS-BOUND STRUCTURE OF NEK2 BOUND TO CCT244858 STRUCTURE OF NEK2 BOUND TO THE AMINOPYRIDINE CCT241950 NEK2-EDE BOUND TO CCT248662 HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND STRUCTURE OF NEK2 BOUND TO AMINIPYRAZINE COMPOUND 5 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 23 HUMAN NEK2 KINASE APO STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 2 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 15 STRUCTURE OF NEK2 BOUND TO CCT243779 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 36 STRUCTURE OF NEK2 BOUND TO CCT242430 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 17 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 35 STRUCTURE OF NEK2 BOUND TO CCT HUMAN NEK2 KINASE ADP-BOUND PDBE Y PDBE 2012-01-19 REL REL GGY 4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{[(1R,2Z)-4,4,4-TRIFLUORO-1-METHYLBUT-2-EN-1-YL]OXY}BENZAMIDE EDO 1,2-ETHANEDIOL HOH water 4A4X PDB ENTRY 4A4X PDB experimental model GGY 1280 2 GGY GGY 1280 A EDO 1281 3 EDO EDO 1281 A HOH 2001 4 HOH HOH 2001 A HOH 2002 4 HOH HOH 2002 A HOH 2003 4 HOH HOH 2003 A HOH 2004 4 HOH HOH 2004 A HOH 2005 4 HOH HOH 2005 A HOH 2006 4 HOH HOH 2006 A HOH 2007 4 HOH HOH 2007 A HOH 2008 4 HOH HOH 2008 A HOH 2009 4 HOH HOH 2009 A HOH 2010 4 HOH HOH 2010 A HOH 2011 4 HOH HOH 2011 A HOH 2012 4 HOH HOH 2012 A HOH 2013 4 HOH HOH 2013 A HOH 2014 4 HOH HOH 2014 A HOH 2015 4 HOH HOH 2015 A HOH 2016 4 HOH HOH 2016 A HOH 2017 4 HOH HOH 2017 A HOH 2018 4 HOH HOH 2018 A HOH 2019 4 HOH HOH 2019 A HOH 2020 4 HOH HOH 2020 A HOH 2021 4 HOH HOH 2021 A HOH 2022 4 HOH HOH 2022 A HOH 2023 4 HOH HOH 2023 A HOH 2024 4 HOH HOH 2024 A HOH 2025 4 HOH HOH 2025 A HOH 2026 4 HOH HOH 2026 A HOH 2027 4 HOH HOH 2027 A HOH 2028 4 HOH HOH 2028 A HOH 2029 4 HOH HOH 2029 A HOH 2030 4 HOH HOH 2030 A HOH 2031 4 HOH HOH 2031 A HOH 2032 4 HOH HOH 2032 A n 1 1 A n 2 2 A SER 3 n 3 SER 3 A ARG 4 n 4 ARG 4 A ALA 5 n 5 ALA 5 A GLU 6 n 6 GLU 6 A ASP 7 n 7 ASP 7 A TYR 8 n 8 TYR 8 A GLU 9 n 9 GLU 9 A VAL 10 n 10 VAL 10 A LEU 11 n 11 LEU 11 A TYR 12 n 12 TYR 12 A THR 13 n 13 THR 13 A ILE 14 n 14 ILE 14 A GLY 15 n 15 GLY 15 A THR 16 n 16 THR 16 A GLY 17 n 17 GLY 17 A SER 18 n 18 SER 18 A TYR 19 n 19 TYR 19 A GLY 20 n 20 GLY 20 A ARG 21 n 21 ARG 21 A CYS 22 n 22 CYS 22 A GLN 23 n 23 GLN 23 A LYS 24 n 24 LYS 24 A ILE 25 n 25 ILE 25 A ARG 26 n 26 ARG 26 A ARG 27 n 27 ARG 27 A LYS 28 n 28 LYS 28 A SER 29 n 29 SER 29 A ASP 30 n 30 ASP 30 A GLY 31 n 31 GLY 31 A LYS 32 n 32 LYS 32 A ILE 33 n 33 ILE 33 A LEU 34 n 34 LEU 34 A VAL 35 n 35 VAL 35 A TRP 36 n 36 TRP 36 A LYS 37 n 37 LYS 37 A GLU 38 n 38 GLU 38 A LEU 39 n 39 LEU 39 A ASP 40 n 40 ASP 40 A TYR 41 n 41 TYR 41 A GLY 42 n 42 GLY 42 A SER 43 n 43 SER 43 A MET 44 n 44 MET 44 A THR 45 n 45 THR 45 A GLU 46 n 46 GLU 46 A ALA 47 n 47 ALA 47 A GLU 48 n 48 GLU 48 A LYS 49 n 49 LYS 49 A GLN 50 n 50 GLN 50 A MET 51 n 51 MET 51 A LEU 52 n 52 LEU 52 A VAL 53 n 53 VAL 53 A SER 54 n 54 SER 54 A GLU 55 n 55 GLU 55 A VAL 56 n 56 VAL 56 A ASN 57 n 57 ASN 57 A LEU 58 n 58 LEU 58 A LEU 59 n 59 LEU 59 A ARG 60 n 60 ARG 60 A GLU 61 n 61 GLU 61 A LEU 62 n 62 LEU 62 A LYS 63 n 63 LYS 63 A HIS 64 n 64 HIS 64 A PRO 65 n 65 PRO 65 A ASN 66 n 66 ASN 66 A ILE 67 n 67 ILE 67 A VAL 68 n 68 VAL 68 A ARG 69 n 69 ARG 69 A TYR 70 n 70 TYR 70 A TYR 71 n 71 TYR 71 A ASP 72 n 72 ASP 72 A ARG 73 n 73 ARG 73 A ILE 74 n 74 ILE 74 A ILE 75 n 75 ILE 75 A ASP 76 n 76 ASP 76 A ARG 77 n 77 ARG 77 A THR 78 n 78 THR 78 A ASN 79 n 79 ASN 79 A THR 80 n 80 THR 80 A THR 81 n 81 THR 81 A LEU 82 n 82 LEU 82 A TYR 83 n 83 TYR 83 A ILE 84 n 84 ILE 84 A VAL 85 n 85 VAL 85 A MET 86 n 86 MET 86 A GLU 87 n 87 GLU 87 A TYR 88 n 88 TYR 88 A CYS 89 n 89 CYS 89 A GLU 90 n 90 GLU 90 A GLY 91 n 91 GLY 91 A GLY 92 n 92 GLY 92 A ASP 93 n 93 ASP 93 A LEU 94 n 94 LEU 94 A ALA 95 n 95 ALA 95 A SER 96 n 96 SER 96 A VAL 97 n 97 VAL 97 A ILE 98 n 98 ILE 98 A THR 99 n 99 THR 99 A LYS 100 n 100 LYS 100 A GLY 101 n 101 GLY 101 A THR 102 n 102 THR 102 A LYS 103 n 103 LYS 103 A GLU 104 n 104 GLU 104 A ARG 105 n 105 ARG 105 A GLN 106 n 106 GLN 106 A TYR 107 n 107 TYR 107 A LEU 108 n 108 LEU 108 A ASP 109 n 109 ASP 109 A GLU 110 n 110 GLU 110 A GLU 111 n 111 GLU 111 A PHE 112 n 112 PHE 112 A VAL 113 n 113 VAL 113 A LEU 114 n 114 LEU 114 A ARG 115 n 115 ARG 115 A VAL 116 n 116 VAL 116 A MET 117 n 117 MET 117 A THR 118 n 118 THR 118 A GLN 119 n 119 GLN 119 A LEU 120 n 120 LEU 120 A THR 121 n 121 THR 121 A LEU 122 n 122 LEU 122 A ALA 123 n 123 ALA 123 A LEU 124 n 124 LEU 124 A LYS 125 n 125 LYS 125 A GLU 126 n 126 GLU 126 A CYS 127 n 127 CYS 127 A HIS 128 n 128 HIS 128 A ARG 129 n 129 ARG 129 A ARG 130 n 130 ARG 130 A SER 131 n 131 SER 131 A n 132 132 A n 133 133 A n 134 134 A n 135 135 A n 136 136 A n 137 137 A n 138 138 A HIS 139 n 139 HIS 139 A ARG 140 n 140 ARG 140 A ASP 141 n 141 ASP 141 A LEU 142 n 142 LEU 142 A LYS 143 n 143 LYS 143 A PRO 144 n 144 PRO 144 A ALA 145 n 145 ALA 145 A ASN 146 n 146 ASN 146 A VAL 147 n 147 VAL 147 A PHE 148 n 148 PHE 148 A LEU 149 n 149 LEU 149 A ASP 150 n 150 ASP 150 A GLY 151 n 151 GLY 151 A LYS 152 n 152 LYS 152 A GLN 153 n 153 GLN 153 A ASN 154 n 154 ASN 154 A VAL 155 n 155 VAL 155 A LYS 156 n 156 LYS 156 A LEU 157 n 157 LEU 157 A GLY 158 n 158 GLY 158 A ASP 159 n 159 ASP 159 A PHE 160 n 160 PHE 160 A GLY 161 n 161 GLY 161 A LEU 162 n 162 LEU 162 A n 163 163 A n 164 164 A n 165 165 A n 166 166 A n 167 167 A n 168 168 A n 169 169 A n 170 170 A n 171 171 A n 172 172 A n 173 173 A n 174 174 A n 175 175 A n 176 176 A VAL 177 n 177 VAL 177 A GLY 178 n 178 GLY 178 A THR 179 n 179 THR 179 A PRO 180 n 180 PRO 180 A TYR 181 n 181 TYR 181 A TYR 182 n 182 TYR 182 A MET 183 n 183 MET 183 A SER 184 n 184 SER 184 A PRO 185 n 185 PRO 185 A GLU 186 n 186 GLU 186 A GLN 187 n 187 GLN 187 A MET 188 n 188 MET 188 A ASN 189 n 189 ASN 189 A ARG 190 n 190 ARG 190 A n 191 191 A n 192 192 A n 193 193 A ASN 194 n 194 ASN 194 A GLU 195 n 195 GLU 195 A LYS 196 n 196 LYS 196 A SER 197 n 197 SER 197 A ASP 198 n 198 ASP 198 A ILE 199 n 199 ILE 199 A TRP 200 n 200 TRP 200 A SER 201 n 201 SER 201 A LEU 202 n 202 LEU 202 A GLY 203 n 203 GLY 203 A CYS 204 n 204 CYS 204 A LEU 205 n 205 LEU 205 A LEU 206 n 206 LEU 206 A TYR 207 n 207 TYR 207 A GLU 208 n 208 GLU 208 A LEU 209 n 209 LEU 209 A CYS 210 n 210 CYS 210 A ALA 211 n 211 ALA 211 A LEU 212 n 212 LEU 212 A MET 213 n 213 MET 213 A PRO 214 n 214 PRO 214 A PRO 215 n 215 PRO 215 A PHE 216 n 216 PHE 216 A THR 217 n 217 THR 217 A ALA 218 n 218 ALA 218 A PHE 219 n 219 PHE 219 A SER 220 n 220 SER 220 A GLN 221 n 221 GLN 221 A LYS 222 n 222 LYS 222 A GLU 223 n 223 GLU 223 A LEU 224 n 224 LEU 224 A ALA 225 n 225 ALA 225 A GLY 226 n 226 GLY 226 A LYS 227 n 227 LYS 227 A ILE 228 n 228 ILE 228 A ARG 229 n 229 ARG 229 A GLU 230 n 230 GLU 230 A GLY 231 n 231 GLY 231 A LYS 232 n 232 LYS 232 A PHE 233 n 233 PHE 233 A ARG 234 n 234 ARG 234 A ARG 235 n 235 ARG 235 A ILE 236 n 236 ILE 236 A PRO 237 n 237 PRO 237 A TYR 238 n 238 TYR 238 A ARG 239 n 239 ARG 239 A TYR 240 n 240 TYR 240 A SER 241 n 241 SER 241 A ASP 242 n 242 ASP 242 A GLU 243 n 243 GLU 243 A LEU 244 n 244 LEU 244 A ASN 245 n 245 ASN 245 A GLU 246 n 246 GLU 246 A ILE 247 n 247 ILE 247 A ILE 248 n 248 ILE 248 A THR 249 n 249 THR 249 A ARG 250 n 250 ARG 250 A MET 251 n 251 MET 251 A LEU 252 n 252 LEU 252 A ASN 253 n 253 ASN 253 A LEU 254 n 254 LEU 254 A LYS 255 n 255 LYS 255 A ASP 256 n 256 ASP 256 A TYR 257 n 257 TYR 257 A HIS 258 n 258 HIS 258 A ARG 259 n 259 ARG 259 A PRO 260 n 260 PRO 260 A SER 261 n 261 SER 261 A VAL 262 n 262 VAL 262 A GLU 263 n 263 GLU 263 A GLU 264 n 264 GLU 264 A ILE 265 n 265 ILE 265 A LEU 266 n 266 LEU 266 A GLU 267 n 267 GLU 267 A ASN 268 n 268 ASN 268 A PRO 269 n 269 PRO 269 A LEU 270 n 270 LEU 270 A ILE 271 n 271 ILE 271 A LEU 272 n 272 LEU 272 A GLU 273 n 273 GLU 273 A HIS 274 n 274 HIS 274 A HIS 275 n 275 HIS 275 A HIS 276 n 276 HIS 276 A HIS 277 n 277 HIS 277 A HIS 278 n 278 HIS 278 A HIS 279 n 279 HIS 279 A 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 A N ILE 14 A N ILE 14 A O CYS 22 A O CYS 22 A N ILE 25 A N ILE 25 A O LEU 34 A O LEU 34 A N LEU 39 A N LEU 39 A O LEU 82 A O LEU 82 A O VAL 85 A O VAL 85 A N TYR 71 A N TYR 71 A N PHE 148 A N PHE 148 A O LYS 156 A O LYS 156 1 A CG LEU 39 A CG LEU 39 1 Y 1 A CD1 LEU 39 A CD1 LEU 39 1 Y 1 A CD2 LEU 39 A CD2 LEU 39 1 Y 1 A CG LYS 63 A CG LYS 63 1 Y 1 A CD LYS 63 A CD LYS 63 1 Y 1 A CE LYS 63 A CE LYS 63 1 Y 1 A NZ LYS 63 A NZ LYS 63 1 Y 1 A CG ASN 79 A CG ASN 79 1 Y 1 A OD1 ASN 79 A OD1 ASN 79 1 Y 1 A ND2 ASN 79 A ND2 ASN 79 1 Y 1 A CG ARG 130 A CG ARG 130 1 Y 1 A CD ARG 130 A CD ARG 130 1 Y 1 A NE ARG 130 A NE ARG 130 1 Y 1 A CZ ARG 130 A CZ ARG 130 1 Y 1 A NH1 ARG 130 A NH1 ARG 130 1 Y 1 A NH2 ARG 130 A NH2 ARG 130 1 Y 1 A CG HIS 139 A CG HIS 139 1 Y 1 A ND1 HIS 139 A ND1 HIS 139 1 Y 1 A CD2 HIS 139 A CD2 HIS 139 1 Y 1 A CE1 HIS 139 A CE1 HIS 139 1 Y 1 A NE2 HIS 139 A NE2 HIS 139 1 Y 1 A CG ARG 190 A CG ARG 190 1 Y 1 A CD ARG 190 A CD ARG 190 1 Y 1 A NE ARG 190 A NE ARG 190 1 Y 1 A CZ ARG 190 A CZ ARG 190 1 Y 1 A NH1 ARG 190 A NH1 ARG 190 1 Y 1 A NH2 ARG 190 A NH2 ARG 190 1 Y 1 A MET 1 A MET 1 1 Y 1 A PRO 2 A PRO 2 1 Y 1 A ASP 132 A ASP 132 1 Y 1 A GLY 133 A GLY 133 1 Y 1 A GLY 134 A GLY 134 1 Y 1 A HIS 135 A HIS 135 1 Y 1 A THR 136 A THR 136 1 Y 1 A VAL 137 A VAL 137 1 Y 1 A LEU 138 A LEU 138 1 Y 1 A ALA 163 A ALA 163 1 Y 1 A ARG 164 A ARG 164 1 Y 1 A ILE 165 A ILE 165 1 Y 1 A LEU 166 A LEU 166 1 Y 1 A ASN 167 A ASN 167 1 Y 1 A HIS 168 A HIS 168 1 Y 1 A ASP 169 A ASP 169 1 Y 1 A THR 170 A THR 170 1 Y 1 A SER 171 A SER 171 1 Y 1 A PHE 172 A PHE 172 1 Y 1 A ALA 173 A ALA 173 1 Y 1 A LYS 174 A LYS 174 1 Y 1 A THR 175 A THR 175 1 Y 1 A PHE 176 A PHE 176 1 Y 1 A MET 191 A MET 191 1 Y 1 A SER 192 A SER 192 1 Y 1 A TYR 193 A TYR 193 1 Y 1 A TYR 12 179.49 170.10 1 A SER 18 60.47 -127.26 1 A ARG 130 -74.42 45.01 1 A ASN 189 -121.14 -103.64 1 A PRO 237 -46.81 152.10 40.06 -8.4693 0.0000 2.7505 2.7340 0.0000 5.7353 0.2482 0.2165 0.2183 2.597 50.286 528 10293 5.1 98.08 0.49 1 1.38 MOLECULAR REPLACEMENT 25.08 0.90 1.11 PDB ENTRY 4A4X ML FLAT BULK SOLVENT MODEL 13.047 0.300 2.597 50.286 32 2131 38 0 2061 0.009 2139 1.110 2882 16.250 818 0.074 309 0.005 366 0.3988 0.3112 2.8586 125 2375 96.00 0.2946 0.2319 3.2721 118 2463 99.00 0.2244 0.1972 4.1223 146 2461 99.00 0.2132 0.1948 50.2953 139 2466 98.00 34.84 2.60 50.29 4AFE 10319 6.0 0.13 1 6.00 2.6 97.4 0.50 2.60 2.73 2.10 1 2.6 87.2 refinement PHENIX (PHENIX.REFINE) data reduction XDS data scaling SCALA phasing PHENIX Nek2 bound to hybrid compound 21 1 N N 2 N N 3 N N 4 N N A ARG 4 A ARG 4 HELX_P A GLU 6 A GLU 6 5 1 3 A THR 45 A THR 45 HELX_P A ARG 60 A ARG 60 1 2 16 A ASP 93 A ASP 93 HELX_P A GLU 104 A GLU 104 1 3 12 A ASP 109 A ASP 109 HELX_P A ARG 130 A ARG 130 1 4 22 A LYS 143 A LYS 143 HELX_P A ALA 145 A ALA 145 5 5 3 A ASN 194 A ASN 194 HELX_P A LEU 212 A LEU 212 1 6 19 A SER 220 A SER 220 HELX_P A GLY 231 A GLY 231 1 7 12 A SER 241 A SER 241 HELX_P A LEU 252 A LEU 252 1 8 12 A LYS 255 A LYS 255 HELX_P A ARG 259 A ARG 259 5 9 5 A SER 261 A SER 261 HELX_P A ASN 268 A ASN 268 1 10 8 A LEU 272 A LEU 272 HELX_P A HIS 276 A HIS 276 5 11 5 TRANSFERASE TRANSFERASE, MITOSIS A GLY 17 A GLY 17 1 A SER 18 A SER 18 5.36 NEK2_HUMAN UNP 1 P51955 1 271 4AFE 1 271 P51955 A 1 1 271 1 expression tag LEU 272 4AFE A P51955 UNP 272 1 expression tag GLU 273 4AFE A P51955 UNP 273 1 expression tag HIS 274 4AFE A P51955 UNP 274 1 expression tag HIS 275 4AFE A P51955 UNP 275 1 expression tag HIS 276 4AFE A P51955 UNP 276 1 expression tag HIS 277 4AFE A P51955 UNP 277 1 expression tag HIS 278 4AFE A P51955 UNP 278 1 expression tag HIS 279 4AFE A P51955 UNP 279 5 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 8 A TYR 8 A THR 16 A THR 16 A ARG 21 A ARG 21 A ARG 27 A ARG 27 A ILE 33 A ILE 33 A ASP 40 A ASP 40 A THR 81 A THR 81 A GLU 87 A GLU 87 A TYR 70 A TYR 70 A ASP 76 A ASP 76 A VAL 147 A VAL 147 A LEU 149 A LEU 149 A VAL 155 A VAL 155 A LEU 157 A LEU 157 BINDING SITE FOR RESIDUE GGY A 1280 A GGY 1280 Software 14 BINDING SITE FOR RESIDUE EDO A 1281 A EDO 1281 Software 3 A TYR 12 A TYR 12 14 1_555 A ILE 14 A ILE 14 14 1_555 A GLY 15 A GLY 15 14 1_555 A TYR 19 A TYR 19 14 1_555 A VAL 35 A VAL 35 14 1_555 A MET 86 A MET 86 14 1_555 A GLU 87 A GLU 87 14 1_555 A TYR 88 A TYR 88 14 1_555 A CYS 89 A CYS 89 14 1_555 A GLU 90 A GLU 90 14 2_555 A GLU 90 A GLU 90 14 1_555 A PHE 148 A PHE 148 14 1_555 A ASP 159 A ASP 159 14 1_555 A PHE 160 A PHE 160 14 1_555 A TYR 19 A TYR 19 3 1_555 A ASP 159 A ASP 159 3 1_555 A PHE 160 A PHE 160 3 1_555 5 C 1 2 1