HEADER LIGASE/LIGASE INHIBITOR 23-AUG-13 4MDN TITLE STRUCTURE OF A NOVEL SUBMICROMOLAR MDM2 INHIBITOR CAVEAT 4MDN LIGAND A Y30 201 HAS DISTORTED GEOMETRY AROUND ITS CA CHIRAL CAVEAT 2 4MDN CENTER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 18-110; COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING COMPND 6 PROTEIN MDM2; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MDM2, P53, CANCER, SMALL MOLECULE, LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.BISTA,G.POPOWICZ,T.A.HOLAK REVDAT 4 28-FEB-24 4MDN 1 REMARK SEQADV REVDAT 3 25-DEC-13 4MDN 1 JRNL REVDAT 2 04-DEC-13 4MDN 1 JRNL REVDAT 1 13-NOV-13 4MDN 0 JRNL AUTH M.BISTA,S.WOLF,K.KHOURY,K.KOWALSKA,Y.HUANG,E.WRONA, JRNL AUTH 2 M.ARCINIEGA,G.M.POPOWICZ,T.A.HOLAK,A.DOMLING JRNL TITL TRANSIENT PROTEIN STATES IN DESIGNING INHIBITORS OF THE JRNL TITL 2 MDM2-P53 INTERACTION. JRNL REF STRUCTURE V. 21 2143 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 24207125 JRNL DOI 10.1016/J.STR.2013.09.006 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 13246 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 50.5622 - 3.2565 0.92 2584 132 0.1573 0.1597 REMARK 3 2 3.2565 - 2.5848 0.95 2546 118 0.1929 0.2253 REMARK 3 3 2.5848 - 2.2581 0.95 2490 152 0.2036 0.2714 REMARK 3 4 2.2581 - 2.0516 0.97 2527 129 0.2133 0.2288 REMARK 3 5 2.0516 - 1.9050 0.94 2441 127 0.2597 0.3301 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 862 REMARK 3 ANGLE : 1.876 1177 REMARK 3 CHIRALITY : 0.102 128 REMARK 3 PLANARITY : 0.008 142 REMARK 3 DIHEDRAL : 13.411 328 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.3209 0.0392 -2.4237 REMARK 3 T TENSOR REMARK 3 T11: 0.2593 T22: 0.1541 REMARK 3 T33: 0.1937 T12: -0.0007 REMARK 3 T13: 0.0031 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 5.3084 L22: 3.9691 REMARK 3 L33: 4.0116 L12: -1.0656 REMARK 3 L13: -0.1636 L23: 1.2356 REMARK 3 S TENSOR REMARK 3 S11: 0.0227 S12: 0.1543 S13: 0.1075 REMARK 3 S21: -0.0242 S22: -0.0112 S23: -0.0117 REMARK 3 S31: -0.0983 S32: -0.1305 S33: -0.0355 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.905 REMARK 200 RESOLUTION RANGE LOW (A) : 50.544 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 20% W/V REMARK 280 PEG3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.84250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.17050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.17050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.42125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.17050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.17050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.26375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.17050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.17050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.42125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.17050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.17050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.26375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.84250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 97 O3 SO4 A 203 4444 2.03 REMARK 500 OG1 THR A 26 ND2 ASN A 79 4444 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 77 32.88 -158.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE Y30 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MDQ RELATED DB: PDB DBREF 4MDN A 18 110 UNP Q00987 MDM2_HUMAN 18 110 SEQADV 4MDN MET A 17 UNP Q00987 INITIATING METHIONINE SEQRES 1 A 94 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 A 94 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 A 94 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 A 94 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 A 94 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 A 94 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 A 94 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 A 94 VAL VAL VAL HET Y30 A 201 40 HET SO4 A 202 5 HET SO4 A 203 5 HETNAM Y30 3-{(1S)-2-(TERT-BUTYLAMINO)-1-[{4-[(4-CHLOROBENZYL) HETNAM 2 Y30 OXY]BENZYL}(FORMYL)AMINO]-2-OXOETHYL}-6-CHLORO-1H- HETNAM 3 Y30 INDOLE-2-CARBOXYLIC ACID HETNAM SO4 SULFATE ION FORMUL 2 Y30 C30 H29 CL2 N3 O5 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *71(H2 O) HELIX 1 1 PRO A 20 GLU A 25 5 6 HELIX 2 2 LYS A 31 VAL A 41 1 11 HELIX 3 3 MET A 50 LYS A 64 1 15 HELIX 4 4 ASP A 80 GLY A 87 1 8 HELIX 5 5 GLU A 95 ARG A 105 1 11 SHEET 1 A 3 TYR A 48 THR A 49 0 SHEET 2 A 3 LEU A 27 PRO A 30 -1 N VAL A 28 O TYR A 48 SHEET 3 A 3 LEU A 107 VAL A 109 -1 O VAL A 108 N ARG A 29 SHEET 1 B 2 ILE A 74 TYR A 76 0 SHEET 2 B 2 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 SITE 1 AC1 13 GLU A 23 LYS A 51 LEU A 54 PHE A 55 SITE 2 AC1 13 GLY A 58 ILE A 61 MET A 62 VAL A 93 SITE 3 AC1 13 HIS A 96 TYR A 100 HOH A 328 HOH A 349 SITE 4 AC1 13 HOH A 356 SITE 1 AC2 4 MET A 17 GLN A 18 HIS A 96 HOH A 342 SITE 1 AC3 2 ARG A 97 HOH A 327 CRYST1 64.341 64.341 81.685 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015542 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015542 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012242 0.00000