0.017837 0.010298 0.000000 0.000000 0.020596 0.000000 0.000000 0.000000 0.009513 0.000000 0.000000 0.000000 0000-0002-8410-3415 Bader, G. 0000-0001-6808-9011 Kessler, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 56.064 56.064 105.119 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 C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C23 H18 Cl2 F N3 O2 458.312 (3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione non-polymer 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 O4 S -2 96.063 SULFATE ION non-polymer C4 H9 N O3 119.119 y THREONINE 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 DE ChemMedChem 1860-7187 14 88 93 10.1002/cmdc.201800617 30458062 Targeted Synthesis of Complex Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-ones by Intramolecular Cyclization of Azomethine Ylides: Highly Potent MDM2-p53 Inhibitors. 2019 100.000 1 N PIXEL 2013-12-05 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 1.00000 1.0 X06SA SLS 1.00000 SYNCHROTRON SLS BEAMLINE X06SA 11011.923 E3 ubiquitin-protein ligase Mdm2 2.3.2.27 1 man polymer 458.312 (3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione 1 syn non-polymer 92.094 GLYCEROL 1 syn non-polymer 96.063 SULFATE ION 2 syn non-polymer 18.015 water 47 nat water Double minute 2 protein,Hdm2,Oncoprotein Mdm2,RING-type E3 ubiquitin transferase Mdm2,p53-binding protein Mdm2 no no QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR KIYTMIYRNLVVVN QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR KIYTMIYRNLVVVN 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 Human sample 1 94 MDM2 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.250 45.480 VAPOR DIFFUSION, HANGING DROP 4.5 2.10 M (NH4)2SO4, 0.10 M Na acetate 293 citation citation_author citation citation_author pdbx_database_proc database_PDB_remark reflns reflns_shell repository Initial release Data collection Database references Data collection Database references Data collection 1 0 2018-12-19 1 1 2018-12-26 1 2 2019-01-16 1 3 2019-03-06 _citation.title _citation_author.identifier_ORCID _citation_author.name _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation_author.identifier_ORCID _database_PDB_remark.text _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs N PDBE Y PDBE 2018-11-07 REL REL H28 (3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione GOL GLYCEROL SO4 SULFATE ION HOH water LIG 1 2 H28 H28 201 A GOL 1 3 GOL GOL 202 A SO4 2 4 SO4 SO4 203 A SO4 3 4 SO4 SO4 204 A HOH 36 5 HOH HOH 301 A HOH 22 5 HOH HOH 302 A HOH 7 5 HOH HOH 303 A HOH 23 5 HOH HOH 304 A HOH 14 5 HOH HOH 305 A HOH 39 5 HOH HOH 306 A HOH 19 5 HOH HOH 307 A HOH 6 5 HOH HOH 308 A HOH 32 5 HOH HOH 309 A HOH 30 5 HOH HOH 310 A HOH 51 5 HOH HOH 311 A HOH 34 5 HOH HOH 312 A HOH 16 5 HOH HOH 313 A HOH 3 5 HOH HOH 314 A HOH 2 5 HOH HOH 315 A HOH 20 5 HOH HOH 316 A HOH 44 5 HOH HOH 317 A HOH 50 5 HOH HOH 318 A HOH 41 5 HOH HOH 319 A HOH 27 5 HOH HOH 320 A HOH 9 5 HOH HOH 321 A HOH 53 5 HOH HOH 322 A HOH 47 5 HOH HOH 323 A HOH 35 5 HOH HOH 324 A HOH 26 5 HOH HOH 325 A HOH 15 5 HOH HOH 326 A HOH 28 5 HOH HOH 327 A HOH 24 5 HOH HOH 328 A HOH 45 5 HOH HOH 329 A HOH 8 5 HOH HOH 330 A HOH 5 5 HOH HOH 331 A HOH 43 5 HOH HOH 332 A HOH 46 5 HOH HOH 333 A HOH 13 5 HOH HOH 334 A HOH 38 5 HOH HOH 335 A HOH 17 5 HOH HOH 336 A HOH 11 5 HOH HOH 337 A HOH 10 5 HOH HOH 338 A HOH 52 5 HOH HOH 339 A HOH 12 5 HOH HOH 340 A HOH 40 5 HOH HOH 341 A HOH 42 5 HOH HOH 342 A HOH 48 5 HOH HOH 343 A HOH 25 5 HOH HOH 344 A HOH 49 5 HOH HOH 345 A HOH 33 5 HOH HOH 346 A HOH 37 5 HOH HOH 347 A GLN 18 n 1 GLN 18 A ILE 19 n 2 ILE 19 A PRO 20 n 3 PRO 20 A ALA 21 n 4 ALA 21 A SER 22 n 5 SER 22 A GLU 23 n 6 GLU 23 A GLN 24 n 7 GLN 24 A GLU 25 n 8 GLU 25 A THR 26 n 9 THR 26 A LEU 27 n 10 LEU 27 A VAL 28 n 11 VAL 28 A ARG 29 n 12 ARG 29 A PRO 30 n 13 PRO 30 A LYS 31 n 14 LYS 31 A PRO 32 n 15 PRO 32 A LEU 33 n 16 LEU 33 A LEU 34 n 17 LEU 34 A LEU 35 n 18 LEU 35 A LYS 36 n 19 LYS 36 A LEU 37 n 20 LEU 37 A LEU 38 n 21 LEU 38 A LYS 39 n 22 LYS 39 A SER 40 n 23 SER 40 A VAL 41 n 24 VAL 41 A GLY 42 n 25 GLY 42 A ALA 43 n 26 ALA 43 A GLN 44 n 27 GLN 44 A LYS 45 n 28 LYS 45 A ASP 46 n 29 ASP 46 A THR 47 n 30 THR 47 A TYR 48 n 31 TYR 48 A THR 49 n 32 THR 49 A MET 50 n 33 MET 50 A LYS 51 n 34 LYS 51 A GLU 52 n 35 GLU 52 A VAL 53 n 36 VAL 53 A LEU 54 n 37 LEU 54 A PHE 55 n 38 PHE 55 A TYR 56 n 39 TYR 56 A LEU 57 n 40 LEU 57 A GLY 58 n 41 GLY 58 A GLN 59 n 42 GLN 59 A TYR 60 n 43 TYR 60 A ILE 61 n 44 ILE 61 A MET 62 n 45 MET 62 A THR 63 n 46 THR 63 A LYS 64 n 47 LYS 64 A ARG 65 n 48 ARG 65 A LEU 66 n 49 LEU 66 A TYR 67 n 50 TYR 67 A ASP 68 n 51 ASP 68 A GLU 69 n 52 GLU 69 A LYS 70 n 53 LYS 70 A GLN 71 n 54 GLN 71 A GLN 72 n 55 GLN 72 A HIS 73 n 56 HIS 73 A ILE 74 n 57 ILE 74 A VAL 75 n 58 VAL 75 A TYR 76 n 59 TYR 76 A CYS 77 n 60 CYS 77 A SER 78 n 61 SER 78 A ASN 79 n 62 ASN 79 A ASP 80 n 63 ASP 80 A LEU 81 n 64 LEU 81 A LEU 82 n 65 LEU 82 A GLY 83 n 66 GLY 83 A ASP 84 n 67 ASP 84 A LEU 85 n 68 LEU 85 A PHE 86 n 69 PHE 86 A GLY 87 n 70 GLY 87 A VAL 88 n 71 VAL 88 A PRO 89 n 72 PRO 89 A SER 90 n 73 SER 90 A PHE 91 n 74 PHE 91 A SER 92 n 75 SER 92 A VAL 93 n 76 VAL 93 A LYS 94 n 77 LYS 94 A GLU 95 n 78 GLU 95 A HIS 96 n 79 HIS 96 A ARG 97 n 80 ARG 97 A LYS 98 n 81 LYS 98 A ILE 99 n 82 ILE 99 A TYR 100 n 83 TYR 100 A THR 101 n 84 THR 101 A MET 102 n 85 MET 102 A ILE 103 n 86 ILE 103 A TYR 104 n 87 TYR 104 A ARG 105 n 88 ARG 105 A ASN 106 n 89 ASN 106 A LEU 107 n 90 LEU 107 A VAL 108 n 91 VAL 108 A VAL 109 n 92 VAL 109 A VAL 110 n 93 VAL 110 A ASN 111 n 94 ASN 111 A author_and_software_defined_assembly PISA 1 monomeric gel filtration 480 -18 6080 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 O TYR 48 A O TYR 31 A N VAL 28 A N VAL 11 A N LEU 27 A N LEU 10 A O VAL 110 A O VAL 93 A N ASP 68 A N ASP 51 A O ILE 74 A O ILE 57 A N VAL 75 A N VAL 58 A O PHE 91 A O PHE 74 1 A A CG CD LYS LYS 70 70 0.228 0.034 1.520 1.748 N 1 A A CB CG GLN GLN 71 71 0.178 0.027 1.521 1.699 N 1 A GLN 71 84.13 68.36 73.820 18.2080 9.500 0.0300 0.0200 0.0000 0.0300 0.0000 -0.0500 0.9590 0.9280 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.2392 0.1884 0.1933 1.7700 48.5500 982 8824 10.0000 96.9600 6.0720 0.0900 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.1410 0.1400 0.8000 0.8000 1.2000 1.7700 48.5500 47 873 25.90 40.34 52 0 774 94 0.011 0.020 846 0.009 0.020 574 1.517 2.062 1156 1.144 3.000 1399 6.549 5.000 97 43.011 23.939 33 12.732 15.000 148 25.184 15.000 4 0.089 0.200 133 0.006 0.021 892 0.001 0.020 164 0.3480 0.0000 0.2950 1.8160 70 525 595 20 95.2000 1.770 48.550 6I3S 9499 0.096 1 23.92 23.100 98.600 0.44 1.800 2.050 1 23.700 97.600 refinement REFMAC 5.6.0117 data extraction PDB_EXTRACT 3.24 data reduction XDS data scaling XSCALE phasing PHASER N E3 ubiquitin-protein ligase Mdm2 (E.C.2.3.2.27) Crystal structure of MDM2 in complex with compound 13. 1 N N 2 N N 3 N N 4 N N 4 N N 5 N N A PRO 20 A PRO 3 HELX_P A GLU 25 A GLU 8 5 AA1 6 A LYS 31 A LYS 14 HELX_P A SER 40 A SER 23 1 AA2 10 A MET 50 A MET 33 HELX_P A LYS 64 A LYS 47 1 AA3 15 A ASP 80 A ASP 63 HELX_P A GLY 87 A GLY 70 1 AA4 8 A GLU 95 A GLU 78 HELX_P A ARG 105 A ARG 88 1 AA5 11 LIGASE Inhibitor, LIGASE MDM2_HUMAN UNP 1 18 Q00987 QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR KIYTMIYRNLVVVN 18 111 6I3S 18 111 Q00987 A 1 1 94 3 3 anti-parallel anti-parallel anti-parallel anti-parallel A TYR 48 A TYR 31 A THR 49 A THR 32 A LEU 27 A LEU 10 A PRO 30 A PRO 13 A LEU 107 A LEU 90 A VAL 110 A VAL 93 A TYR 67 A TYR 50 A ASP 68 A ASP 51 A ILE 74 A ILE 57 A TYR 76 A TYR 59 A SER 90 A SER 73 A SER 92 A SER 75 binding site for residue H28 A 201 A H28 201 Software 11 binding site for residue GOL A 202 A GOL 202 Software 4 binding site for residue SO4 A 203 A SO4 203 Software 7 binding site for residue SO4 A 204 A SO4 204 Software 8 A LEU 54 A LEU 37 11 1_555 A GLY 58 A GLY 41 11 1_555 A ILE 61 A ILE 44 11 1_555 A MET 62 A MET 45 11 1_555 A PHE 86 A PHE 69 11 1_555 A VAL 93 A VAL 76 11 1_555 A HIS 96 A HIS 79 11 1_555 A ILE 99 A ILE 82 11 1_555 A TYR 100 A TYR 83 11 1_555 A HOH 315 F HOH 11 1_555 A HOH 320 F HOH 11 1_555 A ILE 19 A ILE 2 4 1_555 A HIS 96 A HIS 79 4 1_555 A TYR 100 A TYR 83 4 1_555 A HOH 311 F HOH 4 1_555 A GLN 18 A GLN 1 7 1_555 A LYS 94 A LYS 77 7 1_555 A GLU 95 A GLU 78 7 1_555 A HIS 96 A HIS 79 7 1_555 A ARG 97 A ARG 80 7 1_555 A LYS 98 A LYS 81 7 1_555 A HOH 317 F HOH 7 1_555 A ILE 19 A ILE 2 8 6_555 A PRO 20 A PRO 3 8 6_555 A ALA 21 A ALA 4 8 6_555 A LYS 51 A LYS 34 8 12_555 A LYS 51 A LYS 34 8 1_555 A HOH 313 F HOH 8 1_555 A HOH 330 F HOH 8 6_555 A HOH 336 F HOH 8 1_555 178 P 61 2 2