0.017917 0.000000 0.000000 0.000000 0.017917 0.000000 0.000000 0.000000 0.007745 0.00000 0.00000 0.00000 Fradera, X. Uitdehaag, J.C.M. van Zeeland, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 55.814 55.814 129.115 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 C20 H21 F3 N4 374.403 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile non-polymer 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 O4 S -2 96.063 SULFATE ION non-polymer 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 N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O 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 H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O 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 N N 128 N C N 129 N C N 130 N O 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 N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O 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 H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C N 169 N O 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 H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H Y 183 N N Y 184 N C Y 185 N C Y 186 N C Y 187 N N Y 188 N C Y 189 N C N 190 N C N 191 N C N 192 N C N 193 N N Y 194 N C Y 195 N C Y 196 N C Y 197 N C Y 198 N C N 199 N C N 200 N F N 201 N F N 202 N F N 203 N C N 204 N C N 205 N C N 206 N C N 207 N C N 208 N C N 209 N N 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 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 H N 228 N H N 229 N H N 230 N H N 231 N N N 232 S C N 233 N C N 234 N O N 235 N C N 236 N C N 237 N C N 238 N C N 239 N O 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 H N 253 N N N 254 S C N 255 N C N 256 N O N 257 N C N 258 N C N 259 N C N 260 N C N 261 N N N 262 N O 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 H N 275 N H N 276 N H N 277 N H N 278 N N N 279 S C N 280 N C N 281 N O N 282 N C N 283 N C N 284 N S N 285 N C N 286 N O 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 N N 299 S C N 300 N C N 301 N O N 302 N C Y 303 N C Y 304 N C Y 305 N C Y 306 N C Y 307 N C Y 308 N C N 309 N O 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 H N 321 N N N 322 S C N 323 N C N 324 N O N 325 N C N 326 N C 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 N N 339 S C N 340 N C N 341 N O N 342 N C N 343 N O N 344 N O N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N S N 353 N O N 354 N O N 355 N O N 356 N O N 357 N N N 358 S C N 359 N C N 360 N O N 361 R C N 362 N O N 363 N C N 364 N O N 365 N H 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 H N 374 N N N 375 S C N 376 N C N 377 N O N 378 N C Y 379 N C Y 380 N C Y 381 N C Y 382 N N Y 383 N C Y 384 N C Y 385 N C Y 386 N C Y 387 N C N 388 N O N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N N N 402 S C N 403 N C N 404 N O N 405 N C Y 406 N C Y 407 N C Y 408 N C Y 409 N C Y 410 N C Y 411 N C N 412 N O N 413 N O N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N N N 426 S C N 427 N C N 428 N O N 429 N C N 430 N C N 431 N C N 432 N O 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 H N 442 N H N 443 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 doub 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 doub 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 sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub 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 doub N 127 N sing 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 doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 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 doub N 159 N sing 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 sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing Y 173 N doub Y 174 N sing Y 175 N sing Y 176 N sing Y 177 N doub Y 178 N sing N 179 N sing Y 180 N doub N 181 N sing Y 182 N doub Y 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing Y 189 N sing Y 190 N doub N 191 N sing Y 192 N sing Y 193 N doub N 194 N sing 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 trip N 202 N sing N 203 N sing N 204 N sing N 205 N sing 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 sing 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 sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N doub 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 sing N 250 N doub 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 sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub 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 doub N 294 N sing N 295 N sing N 296 N sing N 297 N sing Y 298 N doub Y 299 N sing Y 300 N sing N 301 N sing Y 302 N doub N 303 N sing Y 304 N doub N 305 N sing Y 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 doub N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing 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 doub 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 doub 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 doub N 351 N sing N 352 N sing N 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 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 Y 371 N doub Y 372 N sing Y 373 N sing N 374 N sing Y 375 N doub Y 376 N sing Y 377 N sing N 378 N sing Y 379 N sing Y 380 N doub N 381 N sing Y 382 N doub N 383 N sing Y 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 sing N 394 N doub N 395 N sing N 396 N sing N 397 N sing N 398 N sing Y 399 N doub Y 400 N sing Y 401 N sing N 402 N sing Y 403 N doub N 404 N sing Y 405 N doub N 406 N sing Y 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N doub N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 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 UK Bioorg.Med.Chem.Lett. BMCLE8 1127 0960-894X 20 1524 1527 10.1016/j.bmcl.2010.01.100 20149657 Design and optimization of a series of novel 2-cyano-pyrimidines as cathepsin K inhibitors 2010 10.2210/pdb3kwz/pdb pdb_00003kwz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 CCD 2005-12-12 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.933 1.0 ID14-2 ESRF 0.933 SYNCHROTRON ESRF BEAMLINE ID14-2 23523.480 Cathepsin K 3.4.22.38 UNP residues 115-329 1 man polymer 96.063 SULFATE ION 6 syn non-polymer 374.403 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile 1 syn non-polymer 18.015 water 153 nat water Cathepsin O, Cathepsin X, Cathepsin O2 no no APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 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 human Chinese hamster sample 9606 Homo sapiens ovary cells 10029 Cricetulus griseus 1 2.14 42.45 VAPOR DIFFUSION, HANGING DROP 8.4 26% PEG 4000, 0.1M Tris, 0.2M LiSO4, 15% PEG 400, pH 8.4, VAPOR DIFFUSION, HANGING DROP software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Database references Refinement description Data collection Database references Derived calculations Refinement description 1 0 2010-03-02 1 1 2011-07-13 1 2 2014-02-12 1 3 2017-11-01 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_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.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y PDBJ 2009-12-02 REL REL SO4 SULFATE ION KWZ 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile HOH water In-house cathepsin K structure other SO4 1 2 SO4 SO4 216 A SO4 2 2 SO4 SO4 217 A SO4 3 2 SO4 SO4 218 A SO4 4 2 SO4 SO4 219 A SO4 5 2 SO4 SO4 220 A SO4 6 2 SO4 SO4 221 A 244 1 3 KWZ KWZ 222 A HOH 1 4 HOH HOH 223 A HOH 2 4 HOH HOH 224 A HOH 3 4 HOH HOH 225 A HOH 4 4 HOH HOH 226 A HOH 5 4 HOH HOH 227 A HOH 6 4 HOH HOH 228 A HOH 7 4 HOH HOH 229 A HOH 8 4 HOH HOH 230 A HOH 9 4 HOH HOH 231 A HOH 10 4 HOH HOH 232 A HOH 11 4 HOH HOH 233 A HOH 12 4 HOH HOH 234 A HOH 13 4 HOH HOH 235 A HOH 14 4 HOH HOH 236 A HOH 15 4 HOH HOH 237 A HOH 16 4 HOH HOH 238 A HOH 17 4 HOH HOH 239 A HOH 18 4 HOH HOH 240 A HOH 19 4 HOH HOH 241 A HOH 20 4 HOH HOH 242 A HOH 21 4 HOH HOH 243 A HOH 22 4 HOH HOH 244 A HOH 23 4 HOH HOH 245 A HOH 24 4 HOH HOH 246 A HOH 25 4 HOH HOH 247 A HOH 26 4 HOH HOH 248 A HOH 27 4 HOH HOH 249 A HOH 28 4 HOH HOH 250 A HOH 29 4 HOH HOH 251 A HOH 30 4 HOH HOH 252 A HOH 31 4 HOH HOH 253 A HOH 32 4 HOH HOH 254 A HOH 33 4 HOH HOH 255 A HOH 34 4 HOH HOH 256 A HOH 35 4 HOH HOH 257 A HOH 36 4 HOH HOH 258 A HOH 37 4 HOH HOH 259 A HOH 38 4 HOH HOH 260 A HOH 39 4 HOH HOH 261 A HOH 40 4 HOH HOH 262 A HOH 41 4 HOH HOH 263 A HOH 42 4 HOH HOH 264 A HOH 43 4 HOH HOH 265 A HOH 44 4 HOH HOH 266 A HOH 45 4 HOH HOH 267 A HOH 46 4 HOH HOH 268 A HOH 47 4 HOH HOH 269 A HOH 48 4 HOH HOH 270 A HOH 49 4 HOH HOH 271 A HOH 50 4 HOH HOH 272 A HOH 51 4 HOH HOH 273 A HOH 52 4 HOH HOH 274 A HOH 53 4 HOH HOH 275 A HOH 54 4 HOH HOH 276 A HOH 55 4 HOH HOH 277 A HOH 56 4 HOH HOH 278 A HOH 58 4 HOH HOH 279 A HOH 59 4 HOH HOH 280 A HOH 60 4 HOH HOH 281 A HOH 61 4 HOH HOH 282 A HOH 62 4 HOH HOH 283 A HOH 63 4 HOH HOH 284 A HOH 64 4 HOH HOH 285 A HOH 65 4 HOH HOH 286 A HOH 66 4 HOH HOH 287 A HOH 67 4 HOH HOH 288 A HOH 68 4 HOH HOH 289 A HOH 69 4 HOH HOH 290 A HOH 70 4 HOH HOH 291 A HOH 71 4 HOH HOH 292 A HOH 72 4 HOH HOH 293 A HOH 73 4 HOH HOH 294 A HOH 74 4 HOH HOH 295 A HOH 75 4 HOH HOH 296 A HOH 76 4 HOH HOH 297 A HOH 77 4 HOH HOH 298 A HOH 78 4 HOH HOH 299 A HOH 79 4 HOH HOH 300 A HOH 80 4 HOH HOH 301 A HOH 81 4 HOH HOH 302 A HOH 82 4 HOH HOH 303 A HOH 83 4 HOH HOH 304 A HOH 84 4 HOH HOH 305 A HOH 85 4 HOH HOH 306 A HOH 86 4 HOH HOH 307 A HOH 87 4 HOH HOH 308 A HOH 88 4 HOH HOH 309 A HOH 89 4 HOH HOH 310 A HOH 90 4 HOH HOH 311 A HOH 91 4 HOH HOH 312 A HOH 92 4 HOH HOH 313 A HOH 93 4 HOH HOH 314 A HOH 94 4 HOH HOH 315 A HOH 96 4 HOH HOH 316 A HOH 97 4 HOH HOH 317 A HOH 98 4 HOH HOH 318 A HOH 99 4 HOH HOH 319 A HOH 100 4 HOH HOH 320 A HOH 101 4 HOH HOH 321 A HOH 102 4 HOH HOH 322 A HOH 103 4 HOH HOH 323 A HOH 104 4 HOH HOH 324 A HOH 105 4 HOH HOH 325 A HOH 106 4 HOH HOH 326 A HOH 107 4 HOH HOH 327 A HOH 108 4 HOH HOH 328 A HOH 109 4 HOH HOH 329 A HOH 110 4 HOH HOH 330 A HOH 111 4 HOH HOH 331 A HOH 113 4 HOH HOH 332 A HOH 114 4 HOH HOH 333 A HOH 115 4 HOH HOH 334 A HOH 116 4 HOH HOH 335 A HOH 117 4 HOH HOH 336 A HOH 118 4 HOH HOH 337 A HOH 119 4 HOH HOH 338 A HOH 120 4 HOH HOH 339 A HOH 121 4 HOH HOH 340 A HOH 122 4 HOH HOH 341 A HOH 125 4 HOH HOH 342 A HOH 126 4 HOH HOH 343 A HOH 127 4 HOH HOH 344 A HOH 128 4 HOH HOH 345 A HOH 129 4 HOH HOH 346 A HOH 130 4 HOH HOH 347 A HOH 131 4 HOH HOH 348 A HOH 132 4 HOH HOH 349 A HOH 133 4 HOH HOH 350 A HOH 134 4 HOH HOH 351 A HOH 135 4 HOH HOH 352 A HOH 136 4 HOH HOH 353 A HOH 137 4 HOH HOH 354 A HOH 138 4 HOH HOH 355 A HOH 139 4 HOH HOH 356 A HOH 140 4 HOH HOH 357 A HOH 141 4 HOH HOH 358 A HOH 142 4 HOH HOH 359 A HOH 143 4 HOH HOH 360 A HOH 144 4 HOH HOH 361 A HOH 146 4 HOH HOH 362 A HOH 149 4 HOH HOH 363 A HOH 150 4 HOH HOH 364 A HOH 151 4 HOH HOH 365 A HOH 152 4 HOH HOH 366 A HOH 153 4 HOH HOH 367 A HOH 154 4 HOH HOH 368 A HOH 155 4 HOH HOH 369 A HOH 156 4 HOH HOH 370 A HOH 157 4 HOH HOH 371 A HOH 158 4 HOH HOH 372 A HOH 159 4 HOH HOH 373 A HOH 160 4 HOH HOH 374 A HOH 161 4 HOH HOH 375 A ALA 1 n 1 ALA 1 A PRO 2 n 2 PRO 2 A ASP 3 n 3 ASP 3 A SER 4 n 4 SER 4 A VAL 5 n 5 VAL 5 A ASP 6 n 6 ASP 6 A TYR 7 n 7 TYR 7 A ARG 8 n 8 ARG 8 A LYS 9 n 9 LYS 9 A LYS 10 n 10 LYS 10 A GLY 11 n 11 GLY 11 A TYR 12 n 12 TYR 12 A VAL 13 n 13 VAL 13 A THR 14 n 14 THR 14 A PRO 15 n 15 PRO 15 A VAL 16 n 16 VAL 16 A LYS 17 n 17 LYS 17 A ASN 18 n 18 ASN 18 A GLN 19 n 19 GLN 19 A GLY 20 n 20 GLY 20 A GLN 21 n 21 GLN 21 A CYS 22 n 22 CYS 22 A GLY 23 n 23 GLY 23 A SER 24 n 24 SER 24 A CYS 25 n 25 CYS 25 A TRP 26 n 26 TRP 26 A ALA 27 n 27 ALA 27 A PHE 28 n 28 PHE 28 A SER 29 n 29 SER 29 A SER 30 n 30 SER 30 A VAL 31 n 31 VAL 31 A GLY 32 n 32 GLY 32 A ALA 33 n 33 ALA 33 A LEU 34 n 34 LEU 34 A GLU 35 n 35 GLU 35 A GLY 36 n 36 GLY 36 A GLN 37 n 37 GLN 37 A LEU 38 n 38 LEU 38 A LYS 39 n 39 LYS 39 A LYS 40 n 40 LYS 40 A LYS 41 n 41 LYS 41 A THR 42 n 42 THR 42 A GLY 43 n 43 GLY 43 A LYS 44 n 44 LYS 44 A LEU 45 n 45 LEU 45 A LEU 46 n 46 LEU 46 A ASN 47 n 47 ASN 47 A LEU 48 n 48 LEU 48 A SER 49 n 49 SER 49 A PRO 50 n 50 PRO 50 A GLN 51 n 51 GLN 51 A ASN 52 n 52 ASN 52 A LEU 53 n 53 LEU 53 A VAL 54 n 54 VAL 54 A ASP 55 n 55 ASP 55 A CYS 56 n 56 CYS 56 A VAL 57 n 57 VAL 57 A SER 58 n 58 SER 58 A GLU 59 n 59 GLU 59 A ASN 60 n 60 ASN 60 A ASP 61 n 61 ASP 61 A GLY 62 n 62 GLY 62 A CYS 63 n 63 CYS 63 A GLY 64 n 64 GLY 64 A GLY 65 n 65 GLY 65 A GLY 66 n 66 GLY 66 A TYR 67 n 67 TYR 67 A MET 68 n 68 MET 68 A THR 69 n 69 THR 69 A ASN 70 n 70 ASN 70 A ALA 71 n 71 ALA 71 A PHE 72 n 72 PHE 72 A GLN 73 n 73 GLN 73 A TYR 74 n 74 TYR 74 A VAL 75 n 75 VAL 75 A GLN 76 n 76 GLN 76 A LYS 77 n 77 LYS 77 A ASN 78 n 78 ASN 78 A ARG 79 n 79 ARG 79 A GLY 80 n 80 GLY 80 A ILE 81 n 81 ILE 81 A ASP 82 n 82 ASP 82 A SER 83 n 83 SER 83 A GLU 84 n 84 GLU 84 A ASP 85 n 85 ASP 85 A ALA 86 n 86 ALA 86 A TYR 87 n 87 TYR 87 A PRO 88 n 88 PRO 88 A TYR 89 n 89 TYR 89 A VAL 90 n 90 VAL 90 A GLY 91 n 91 GLY 91 A GLN 92 n 92 GLN 92 A GLU 93 n 93 GLU 93 A GLU 94 n 94 GLU 94 A SER 95 n 95 SER 95 A CYS 96 n 96 CYS 96 A MET 97 n 97 MET 97 A TYR 98 n 98 TYR 98 A ASN 99 n 99 ASN 99 A PRO 100 n 100 PRO 100 A THR 101 n 101 THR 101 A GLY 102 n 102 GLY 102 A LYS 103 n 103 LYS 103 A ALA 104 n 104 ALA 104 A ALA 105 n 105 ALA 105 A LYS 106 n 106 LYS 106 A CYS 107 n 107 CYS 107 A ARG 108 n 108 ARG 108 A GLY 109 n 109 GLY 109 A TYR 110 n 110 TYR 110 A ARG 111 n 111 ARG 111 A GLU 112 n 112 GLU 112 A ILE 113 n 113 ILE 113 A PRO 114 n 114 PRO 114 A GLU 115 n 115 GLU 115 A GLY 116 n 116 GLY 116 A ASN 117 n 117 ASN 117 A GLU 118 n 118 GLU 118 A LYS 119 n 119 LYS 119 A ALA 120 n 120 ALA 120 A LEU 121 n 121 LEU 121 A LYS 122 n 122 LYS 122 A ARG 123 n 123 ARG 123 A ALA 124 n 124 ALA 124 A VAL 125 n 125 VAL 125 A ALA 126 n 126 ALA 126 A ARG 127 n 127 ARG 127 A VAL 128 n 128 VAL 128 A GLY 129 n 129 GLY 129 A PRO 130 n 130 PRO 130 A VAL 131 n 131 VAL 131 A SER 132 n 132 SER 132 A VAL 133 n 133 VAL 133 A ALA 134 n 134 ALA 134 A ILE 135 n 135 ILE 135 A ASP 136 n 136 ASP 136 A ALA 137 n 137 ALA 137 A SER 138 n 138 SER 138 A LEU 139 n 139 LEU 139 A THR 140 n 140 THR 140 A SER 141 n 141 SER 141 A PHE 142 n 142 PHE 142 A GLN 143 n 143 GLN 143 A PHE 144 n 144 PHE 144 A TYR 145 n 145 TYR 145 A SER 146 n 146 SER 146 A LYS 147 n 147 LYS 147 A GLY 148 n 148 GLY 148 A VAL 149 n 149 VAL 149 A TYR 150 n 150 TYR 150 A TYR 151 n 151 TYR 151 A ASP 152 n 152 ASP 152 A GLU 153 n 153 GLU 153 A SER 154 n 154 SER 154 A CYS 155 n 155 CYS 155 A ASN 156 n 156 ASN 156 A SER 157 n 157 SER 157 A ASP 158 n 158 ASP 158 A ASN 159 n 159 ASN 159 A LEU 160 n 160 LEU 160 A ASN 161 n 161 ASN 161 A HIS 162 n 162 HIS 162 A ALA 163 n 163 ALA 163 A VAL 164 n 164 VAL 164 A LEU 165 n 165 LEU 165 A ALA 166 n 166 ALA 166 A VAL 167 n 167 VAL 167 A GLY 168 n 168 GLY 168 A TYR 169 n 169 TYR 169 A GLY 170 n 170 GLY 170 A ILE 171 n 171 ILE 171 A GLN 172 n 172 GLN 172 A LYS 173 n 173 LYS 173 A GLY 174 n 174 GLY 174 A ASN 175 n 175 ASN 175 A LYS 176 n 176 LYS 176 A HIS 177 n 177 HIS 177 A TRP 178 n 178 TRP 178 A ILE 179 n 179 ILE 179 A ILE 180 n 180 ILE 180 A LYS 181 n 181 LYS 181 A ASN 182 n 182 ASN 182 A SER 183 n 183 SER 183 A TRP 184 n 184 TRP 184 A GLY 185 n 185 GLY 185 A GLU 186 n 186 GLU 186 A ASN 187 n 187 ASN 187 A TRP 188 n 188 TRP 188 A GLY 189 n 189 GLY 189 A ASN 190 n 190 ASN 190 A LYS 191 n 191 LYS 191 A GLY 192 n 192 GLY 192 A TYR 193 n 193 TYR 193 A ILE 194 n 194 ILE 194 A LEU 195 n 195 LEU 195 A MET 196 n 196 MET 196 A ALA 197 n 197 ALA 197 A ARG 198 n 198 ARG 198 A ASN 199 n 199 ASN 199 A LYS 200 n 200 LYS 200 A ASN 201 n 201 ASN 201 A ASN 202 n 202 ASN 202 A ALA 203 n 203 ALA 203 A CYS 204 n 204 CYS 204 A GLY 205 n 205 GLY 205 A ILE 206 n 206 ILE 206 A ALA 207 n 207 ALA 207 A ASN 208 n 208 ASN 208 A LEU 209 n 209 LEU 209 A ALA 210 n 210 ALA 210 A SER 211 n 211 SER 211 A PHE 212 n 212 PHE 212 A PRO 213 n 213 PRO 213 A LYS 214 n 214 LYS 214 A MET 215 n 215 MET 215 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 VAL 5 A N VAL 5 A O TYR 169 A O TYR 169 A O ALA 166 A O ALA 166 A N VAL 131 A N VAL 131 A N VAL 5 A N VAL 5 A O TYR 169 A O TYR 169 A N VAL 167 A N VAL 167 A O ILE 179 A O ILE 179 A N TRP 178 A N TRP 178 A O MET 196 A O MET 196 A O LEU 195 A O LEU 195 A N TYR 150 A N TYR 150 A N ILE 81 A N ILE 81 A O ALA 104 A O ALA 104 A N ARG 111 A N ARG 111 A O PHE 212 A O PHE 212 1 A A NZ O LYS ASN 41 187 2.15 B 1_555 4_545 1 A TYR 87 -152.41 77.97 1 A SER 146 -131.84 -32.64 1 A LEU 209 -144.57 57.60 22.048 0.61 0.00 0.00 0.61 0.00 -1.22 0.954 0.916 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.29878 0.23554 0.23863 1.49 42.22 1398 28061 26506 5.0 81.93 4.709 0.147 RANDOM 1 isotropic THROUGHOUT 1.0 MOLECULAR REPLACEMENT 0.121 0.129 0.80 0.80 1.40 In-house cathepsin K structure MAXIMUM LIKELIHOOD MASK 1.49 42.22 153 1859 57 0 1649 0.021 0.022 1771 0.001 0.020 1216 1.852 1.978 2398 1.118 3.005 2955 6.313 5.000 222 33.293 25.000 80 16.253 15.000 296 8.927 15.000 8 0.098 0.200 237 0.007 0.020 1981 0.001 0.020 351 0.190 0.200 321 0.193 0.200 1209 0.176 0.200 817 0.093 0.200 878 0.194 0.200 103 0.141 0.200 17 0.255 0.200 49 0.275 0.200 12 1.229 1.500 1382 0.257 1.500 450 1.430 2.000 1705 2.545 3.000 851 3.443 4.500 689 0.577 0.550 1.532 19 417 20 17.63 16.5 1.49 51.23 3KWZ 28061 28061 0 0 0.132 1 8 10.26 81.8 0.132 1.49 1.54 0.7 1 1.78 19.7 data collection CrystalClear refinement REFMAC 5.2.0019 data reduction CrystalClear data scaling CrystalClear Cathepsin K in complex with a non-selective 2-cyano-pyrimidine inhibitor 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 4 N N A SER 24 A SER 24 HELX_P A GLY 43 A GLY 43 1 1 20 A SER 49 A SER 49 HELX_P A VAL 57 A VAL 57 1 2 9 A ASP 61 A ASP 61 HELX_P A GLY 65 A GLY 65 5 3 5 A TYR 67 A TYR 67 HELX_P A ARG 79 A ARG 79 1 4 13 A ASN 99 A ASN 99 HELX_P A THR 101 A THR 101 5 5 3 A ASN 117 A ASN 117 HELX_P A VAL 128 A VAL 128 1 6 12 A LEU 139 A LEU 139 HELX_P A PHE 144 A PHE 144 1 7 6 A ASN 202 A ASN 202 HELX_P A ILE 206 A ILE 206 5 8 5 disulf 1.971 A CYS 22 A SG CYS 22 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.024 A CYS 56 A SG CYS 56 1_555 A CYS 96 A SG CYS 96 1_555 disulf 2.066 A CYS 155 A SG CYS 155 1_555 A CYS 204 A SG CYS 204 1_555 covale 1.783 none A CYS 25 A SG CYS 25 1_555 A KWZ 222 H C26 KWZ 1_555 HYDROLASE cathepsin K, enzyme inhibitor, covalent reversible inhibitor, Disease mutation, Disulfide bond, Glycoprotein, Hydrolase, Lysosome, Protease, Thiol protease, Zymogen CATK_HUMAN UNP 1 115 P43235 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRG IDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNL NHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 115 329 3KWZ 1 215 P43235 A 1 1 215 3 5 2 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel A VAL 5 A VAL 5 A ASP 6 A ASP 6 A HIS 162 A HIS 162 A GLN 172 A GLN 172 A VAL 131 A VAL 131 A ILE 135 A ILE 135 A VAL 5 A VAL 5 A ASP 6 A ASP 6 A HIS 162 A HIS 162 A GLN 172 A GLN 172 A ASN 175 A ASN 175 A LYS 181 A LYS 181 A TYR 193 A TYR 193 A ALA 197 A ALA 197 A VAL 149 A VAL 149 A TYR 150 A TYR 150 A ILE 81 A ILE 81 A ASP 82 A ASP 82 A LYS 103 A LYS 103 A ALA 105 A ALA 105 A TYR 110 A TYR 110 A GLU 112 A GLU 112 A SER 211 A SER 211 A PRO 213 A PRO 213 BINDING SITE FOR RESIDUE SO4 A 216 A SO4 216 Software 7 BINDING SITE FOR RESIDUE SO4 A 217 A SO4 217 Software 7 BINDING SITE FOR RESIDUE SO4 A 218 A SO4 218 Software 5 BINDING SITE FOR RESIDUE SO4 A 219 A SO4 219 Software 7 BINDING SITE FOR RESIDUE SO4 A 220 A SO4 220 Software 6 BINDING SITE FOR RESIDUE SO4 A 221 A SO4 221 Software 6 BINDING SITE FOR RESIDUE KWZ A 222 A KWZ 222 Software 15 A GLN 19 A GLN 19 7 1_555 A ARG 127 A ARG 127 7 3_444 A HIS 162 A HIS 162 7 1_555 A TRP 184 A TRP 184 7 1_555 A KWZ 222 H KWZ 7 1_555 A HOH 244 I HOH 7 1_555 A HOH 277 I HOH 7 1_555 A ASN 18 A ASN 18 7 1_555 A ARG 111 A ARG 111 7 3_444 A GLY 185 A GLY 185 7 1_555 A GLU 186 A GLU 186 7 1_555 A ASN 187 A ASN 187 7 1_555 A LYS 214 A LYS 214 7 3_444 A HOH 337 I HOH 7 1_555 A PRO 2 A PRO 2 5 3_444 A ASP 3 A ASP 3 5 3_444 A LEU 139 A LEU 139 5 1_555 A THR 140 A THR 140 5 1_555 A SER 141 A SER 141 5 1_555 A LYS 10 A LYS 10 7 3_444 A PHE 144 A PHE 144 7 1_555 A TYR 145 A TYR 145 7 1_555 A SER 146 A SER 146 7 1_555 A LYS 147 A LYS 147 7 1_555 A HOH 275 I HOH 7 1_555 A HOH 286 I HOH 7 3_444 A GLN 92 A GLN 92 6 1_555 A GLU 93 A GLU 93 6 1_555 A LYS 173 A LYS 173 6 7_655 A HOH 271 I HOH 6 1_555 A HOH 316 I HOH 6 1_555 A HOH 354 I HOH 6 1_555 A ASN 117 A ASN 117 6 1_555 A LYS 119 A LYS 119 6 1_555 A ARG 123 A ARG 123 6 1_555 A HOH 260 I HOH 6 4_545 A HOH 320 I HOH 6 1_555 A HOH 375 I HOH 6 1_555 A GLN 19 A GLN 19 15 1_555 A GLY 23 A GLY 23 15 1_555 A CYS 25 A CYS 25 15 1_555 A GLY 64 A GLY 64 15 1_555 A GLY 65 A GLY 65 15 1_555 A GLY 66 A GLY 66 15 1_555 A TYR 67 A TYR 67 15 1_555 A MET 68 A MET 68 15 1_555 A ALA 134 A ALA 134 15 1_555 A LEU 160 A LEU 160 15 1_555 A ASN 161 A ASN 161 15 1_555 A HIS 162 A HIS 162 15 1_555 A ALA 163 A ALA 163 15 1_555 A LEU 209 A LEU 209 15 1_555 A SO4 216 B SO4 15 1_555 96 P 43 21 2