0.013972 0.000000 0.000000 -0.000000 0.013972 0.000000 0.000000 -0.000000 0.009464 0.00000 0.00000 0.00000 Chessari, G. Buck, I.M. Day, J.E.H. Day, P.J. Iqbal, A. Johnson, C.N. Lewis, E.J. Martins, V. Miller, D. Reader, M. Rees, D.C. Rich, S.J. Tamanini, E. Vitorino, M. Ward, G.A. Williams, P.A. Williams, G. Wilsher, N.E. Woolford, A.J.-A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 71.571 71.571 105.666 C8 H13 Br N3 1 231.113 4-(4-bromo-1H-pyrazol-1-yl)piperidinium 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 Zn 2 65.409 ZINC ION non-polymer US J.Med.Chem. JMCMAR 0151 0022-2623 58 6574 6588 10.1021/acs.jmedchem.5b00706 26218264 Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Discovery of a Non-Alanine Lead Series with Dual Activity Against cIAP1 and XIAP. 2015 100 1 CCD 2008-10-08 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 .9834 1.0 ID23-1 ESRF .9834 SYNCHROTRON ESRF BEAMLINE ID23-1 12686.206 E3 ubiquitin-protein ligase XIAP 6.3.2.- residues 245-354 1 man polymer 65.409 ZINC ION 1 syn non-polymer 231.113 4-(4-bromo-1H-pyrazol-1-yl)piperidinium 1 syn non-polymer 18.015 water 56 nat water Baculoviral IAP repeat-containing protein 4,IAP-like protein,hILP,Inhibitor of apoptosis protein 3,hIAP3,X-linked inhibitor of apoptosis protein,X-linked IAP no no GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY PGCKYLLEQKGQEYINNIHLTHSLEECLVR GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY PGCKYLLEQKGQEYINNIHLTHSLEECLVR 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 Human Image clone sample 1 110 XIAP, API3, BIRC4, IAP3 9606 Homo sapiens 469008 Escherichia coli BL21(DE3) Biological sequence pET 28b 2.32 1.35 47 Blocks VAPOR DIFFUSION, HANGING DROP 7.5 3.9M NaCl, 0.1M HEPES/NaOHpH=7.5 277 repository Initial release Database references 1 0 2015-08-12 1 1 2015-09-09 5C0K contains the same protein but with a different ligand N RCSB Y PDBE 2015-06-12 REL REL 1 A O HOH 556 6.00 ZN ZINC ION 4WJ 4-(4-bromo-1H-pyrazol-1-yl)piperidinium HOH water ZN 1 2 ZN ZN 401 A L01 1 3 4WJ 4WJ 402 A HOH 8 4 HOH HOH 501 A HOH 3 4 HOH HOH 502 A HOH 54 4 HOH HOH 503 A HOH 1 4 HOH HOH 504 A HOH 18 4 HOH HOH 505 A HOH 53 4 HOH HOH 506 A HOH 13 4 HOH HOH 507 A HOH 42 4 HOH HOH 508 A HOH 44 4 HOH HOH 509 A HOH 36 4 HOH HOH 510 A HOH 38 4 HOH HOH 511 A HOH 40 4 HOH HOH 512 A HOH 43 4 HOH HOH 513 A HOH 55 4 HOH HOH 514 A HOH 33 4 HOH HOH 515 A HOH 5 4 HOH HOH 516 A HOH 39 4 HOH HOH 517 A HOH 34 4 HOH HOH 518 A HOH 26 4 HOH HOH 519 A HOH 56 4 HOH HOH 520 A HOH 2 4 HOH HOH 521 A HOH 27 4 HOH HOH 522 A HOH 32 4 HOH HOH 523 A HOH 59 4 HOH HOH 524 A HOH 6 4 HOH HOH 525 A HOH 20 4 HOH HOH 526 A HOH 31 4 HOH HOH 527 A HOH 16 4 HOH HOH 528 A HOH 63 4 HOH HOH 529 A HOH 30 4 HOH HOH 530 A HOH 52 4 HOH HOH 531 A HOH 25 4 HOH HOH 532 A HOH 7 4 HOH HOH 533 A HOH 51 4 HOH HOH 534 A HOH 65 4 HOH HOH 535 A HOH 14 4 HOH HOH 536 A HOH 21 4 HOH HOH 537 A HOH 66 4 HOH HOH 538 A HOH 12 4 HOH HOH 539 A HOH 15 4 HOH HOH 540 A HOH 47 4 HOH HOH 541 A HOH 17 4 HOH HOH 542 A HOH 11 4 HOH HOH 543 A HOH 35 4 HOH HOH 544 A HOH 4 4 HOH HOH 545 A HOH 19 4 HOH HOH 546 A HOH 23 4 HOH HOH 547 A HOH 24 4 HOH HOH 548 A HOH 9 4 HOH HOH 549 A HOH 67 4 HOH HOH 550 A HOH 50 4 HOH HOH 551 A HOH 62 4 HOH HOH 552 A HOH 61 4 HOH HOH 553 A HOH 22 4 HOH HOH 554 A HOH 64 4 HOH HOH 555 A HOH 29 4 HOH HOH 556 A n 1 245 A n 2 246 A n 3 247 A n 4 248 A ASN 249 n 5 ASN 249 A PHE 250 n 6 PHE 250 A PRO 251 n 7 PRO 251 A ASN 252 n 8 ASN 252 A SER 253 n 9 SER 253 A THR 254 n 10 THR 254 A ASN 255 n 11 ASN 255 A LEU 256 n 12 LEU 256 A PRO 257 n 13 PRO 257 A ARG 258 n 14 ARG 258 A ASN 259 n 15 ASN 259 A PRO 260 n 16 PRO 260 A SER 261 n 17 SER 261 A MET 262 n 18 MET 262 A ALA 263 n 19 ALA 263 A ASP 264 n 20 ASP 264 A TYR 265 n 21 TYR 265 A GLU 266 n 22 GLU 266 A ALA 267 n 23 ALA 267 A ARG 268 n 24 ARG 268 A ILE 269 n 25 ILE 269 A PHE 270 n 26 PHE 270 A THR 271 n 27 THR 271 A PHE 272 n 28 PHE 272 A GLY 273 n 29 GLY 273 A THR 274 n 30 THR 274 A TRP 275 n 31 TRP 275 A ILE 276 n 32 ILE 276 A TYR 277 n 33 TYR 277 A SER 278 n 34 SER 278 A VAL 279 n 35 VAL 279 A ASN 280 n 36 ASN 280 A LYS 281 n 37 LYS 281 A GLU 282 n 38 GLU 282 A GLN 283 n 39 GLN 283 A LEU 284 n 40 LEU 284 A ALA 285 n 41 ALA 285 A ARG 286 n 42 ARG 286 A ALA 287 n 43 ALA 287 A GLY 288 n 44 GLY 288 A PHE 289 n 45 PHE 289 A TYR 290 n 46 TYR 290 A ALA 291 n 47 ALA 291 A LEU 292 n 48 LEU 292 A GLY 293 n 49 GLY 293 A GLU 294 n 50 GLU 294 A GLY 295 n 51 GLY 295 A ASP 296 n 52 ASP 296 A LYS 297 n 53 LYS 297 A VAL 298 n 54 VAL 298 A LYS 299 n 55 LYS 299 A CYS 300 n 56 CYS 300 A PHE 301 n 57 PHE 301 A HIS 302 n 58 HIS 302 A CYS 303 n 59 CYS 303 A GLY 304 n 60 GLY 304 A GLY 305 n 61 GLY 305 A GLY 306 n 62 GLY 306 A LEU 307 n 63 LEU 307 A THR 308 n 64 THR 308 A ASP 309 n 65 ASP 309 A TRP 310 n 66 TRP 310 A LYS 311 n 67 LYS 311 A PRO 312 n 68 PRO 312 A SER 313 n 69 SER 313 A GLU 314 n 70 GLU 314 A ASP 315 n 71 ASP 315 A PRO 316 n 72 PRO 316 A TRP 317 n 73 TRP 317 A GLU 318 n 74 GLU 318 A GLN 319 n 75 GLN 319 A HIS 320 n 76 HIS 320 A ALA 321 n 77 ALA 321 A LYS 322 n 78 LYS 322 A TRP 323 n 79 TRP 323 A TYR 324 n 80 TYR 324 A PRO 325 n 81 PRO 325 A GLY 326 n 82 GLY 326 A CYS 327 n 83 CYS 327 A LYS 328 n 84 LYS 328 A TYR 329 n 85 TYR 329 A LEU 330 n 86 LEU 330 A LEU 331 n 87 LEU 331 A GLU 332 n 88 GLU 332 A GLN 333 n 89 GLN 333 A LYS 334 n 90 LYS 334 A GLY 335 n 91 GLY 335 A GLN 336 n 92 GLN 336 A GLU 337 n 93 GLU 337 A TYR 338 n 94 TYR 338 A ILE 339 n 95 ILE 339 A ASN 340 n 96 ASN 340 A ASN 341 n 97 ASN 341 A ILE 342 n 98 ILE 342 A HIS 343 n 99 HIS 343 A LEU 344 n 100 LEU 344 A THR 345 n 101 THR 345 A HIS 346 n 102 HIS 346 A SER 347 n 103 SER 347 A LEU 348 n 104 LEU 348 A GLU 349 n 105 GLU 349 A GLU 350 n 106 GLU 350 A CYS 351 n 107 CYS 351 A LEU 352 n 108 LEU 352 A VAL 353 n 109 VAL 353 A ARG 354 n 110 ARG 354 A 6.7377 -0.8019 1.0612 2.7624 -0.6141 3.5585 0.1032 -0.3739 0.0479 0.3117 -0.0476 0.0561 -0.0985 -0.0020 -0.0556 0.0419 -0.0181 0.0093 0.0809 -0.0296 0.0129 refined -17.3482 -28.7670 -4.0275 X-RAY DIFFRACTION A 249 A 354 X-RAY DIFFRACTION 1 software_defined_assembly PISA 1 monomeric 0 0 6670 A CYS 300 A SG CYS 56 1_555 A ZN 401 B ZN ZN 1_555 A CYS 303 A SG CYS 59 1_555 106.5 A CYS 300 A SG CYS 56 1_555 A ZN 401 B ZN ZN 1_555 A HIS 320 A NE2 HIS 76 1_555 99.8 A CYS 303 A SG CYS 59 1_555 A ZN 401 B ZN ZN 1_555 A HIS 320 A NE2 HIS 76 1_555 112.4 A CYS 300 A SG CYS 56 1_555 A ZN 401 B ZN ZN 1_555 A CYS 327 A SG CYS 83 1_555 118.9 A CYS 303 A SG CYS 59 1_555 A ZN 401 B ZN ZN 1_555 A CYS 327 A SG CYS 83 1_555 113.4 A HIS 320 A NE2 HIS 76 1_555 A ZN 401 B ZN ZN 1_555 A CYS 327 A SG CYS 83 1_555 105.1 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 TYR 290 A N TYR 46 A O LYS 299 A O LYS 55 A N VAL 298 A N VAL 54 A O LEU 307 A O LEU 63 1 A HOH 541 D HOH 1 A GLY 245 A GLY 1 1 Y 1 A SER 246 A SER 2 1 Y 1 A HIS 247 A HIS 3 1 Y 1 A MET 248 A MET 4 1 Y 1 A CYS 351 -73.65 44.49 45.118 0.66 -0.00 -0.00 0.66 -0.00 -1.32 0.934 0.904 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 0.23234 0.19979 0.20144 2.60 71.57 473 8443 5.3 99.38 11.222 0.136 RANDOM 1 THROUGHOUT 0.236 0.205 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.60 71.57 56 935 13 0 866 0.011 0.019 907 0.009 0.027 13 1.419 1.924 1230 0.188 1.072 32 5.319 5.000 105 36.855 24.255 47 18.622 15.000 148 12.281 15.000 4 0.118 0.200 118 0.000 0.021 718 0.000 0.013 2 2.528 6.381 423 4.393 7.120 481 4.388 7.121 482 11.434 14.956 304 0.252 0.291 2.666 35 612 20 99.39 2.59 71.57 5C0L 8972 8972 2.0 0.071 1 7.8 3.6 99.5 0.335 2.59 2.63 2.2 1 99.5 refinement REFMAC 5.8.0107 E3 ubiquitin-protein ligase XIAP (E.C.6.3.2.-) Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 2 1 N N 2 N N 3 N N 4 N N A ASN 259 A ASN 15 HELX_P A ALA 263 A ALA 19 5 AA1 5 A ASP 264 A ASP 20 HELX_P A THR 271 A THR 27 1 AA2 8 A ASN 280 A ASN 36 HELX_P A ALA 287 A ALA 43 1 AA3 8 A ASP 315 A ASP 71 HELX_P A TYR 324 A TYR 80 1 AA4 10 A CYS 327 A CYS 83 HELX_P A CYS 351 A CYS 107 1 AA5 25 metalc 2.247 A CYS 300 A SG CYS 56 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.307 A CYS 303 A SG CYS 59 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.148 A HIS 320 A NE2 HIS 76 1_555 A ZN 401 B ZN ZN 1_555 metalc 2.343 A CYS 327 A SG CYS 83 1_555 A ZN 401 B ZN ZN 1_555 LIGASE ligase XIAP_HUMAN UNP 1 245 P98170 SSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY PGCKYLLEQKGQEYINNIHLTHSLEECLVR 245 354 5C0L 245 354 P98170 A 1 1 110 1 SER conflict GLY 245 5C0L A P98170 UNP 245 1 1 ASP conflict HIS 247 5C0L A P98170 UNP 247 3 1 ARG conflict MET 248 5C0L A P98170 UNP 248 4 3 anti-parallel anti-parallel A PHE 289 A PHE 45 A ALA 291 A ALA 47 A VAL 298 A VAL 54 A CYS 300 A CYS 56 A GLY 306 A GLY 62 A LEU 307 A LEU 63 binding site for residue ZN A 401 A ZN 401 Software 4 binding site for residue 4WJ A 402 A 4WJ 402 Software 6 A CYS 300 A CYS 56 4 1_555 A CYS 303 A CYS 59 4 1_555 A HIS 320 A HIS 76 4 1_555 A CYS 327 A CYS 83 4 1_555 A LEU 307 A LEU 63 6 1_555 A THR 308 A THR 64 6 1_555 A ASP 309 A ASP 65 6 1_555 A GLU 314 A GLU 70 6 1_555 A GLN 319 A GLN 75 6 1_555 A TRP 323 A TRP 79 6 1_555 91 P 41 2 2