HEADER LIGASE/LIGASE INHIBITOR 25-MAR-13 4JVE TITLE CO-CRYSTAL STRUCTURE OF MDM2 WITH INHIBITOR (2R,3E)-2-[(2S,3R,6S)-2,3- TITLE 2 BIS(4-CHLOROPHENYL)-6-(4-FLUOROBENZYL)-5-OXOMORPHOLIN-4-YL]PENT-3- TITLE 3 ENOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 18-111; 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 P53, PROTEIN-PROTEIN INTERACTION, LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.HUANG,F.GONZALEZ-LOPEZ DE TURISO,D.SUN,R.YOSUP,M.D.BARTBERGER, AUTHOR 2 H.P.BECK,J.CANNON,P.SHAFFER,J.D.OLINER,S.H.OLSON,J.C.MEDINA REVDAT 3 06-NOV-24 4JVE 1 REMARK SEQADV REVDAT 2 05-JUN-13 4JVE 1 JRNL REVDAT 1 01-MAY-13 4JVE 0 JRNL AUTH F.GONZALEZ-LOPEZ DE TURISO,D.SUN,Y.REW,M.D.BARTBERGER, JRNL AUTH 2 H.P.BECK,J.CANON,A.CHEN,D.CHOW,T.L.CORRELL,X.HUANG, JRNL AUTH 3 L.D.JULIAN,F.KAYSER,M.C.LO,A.M.LONG,D.MCMINN,J.D.OLINER, JRNL AUTH 4 T.OSGOOD,J.P.POWERS,A.Y.SAIKI,S.SCHNEIDER,P.SHAFFER, JRNL AUTH 5 S.H.XIAO,P.YAKOWEC,X.YAN,Q.YE,D.YU,X.ZHAO,J.ZHOU,J.C.MEDINA, JRNL AUTH 6 S.H.OLSON JRNL TITL RATIONAL DESIGN AND BINDING MODE DUALITY OF MDM2-P53 JRNL TITL 2 INHIBITORS. JRNL REF J.MED.CHEM. V. 56 4053 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23597064 JRNL DOI 10.1021/JM400293Z REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5147 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 238 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.92600 REMARK 3 B22 (A**2) : 0.92600 REMARK 3 B33 (A**2) : -1.85200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.511 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.358 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.234 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.318 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : MDM2.PARAM REMARK 3 PARAMETER FILE 2 : 2206089.XPRM REMARK 3 PARAMETER FILE 3 : MSI_CNX_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F 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 : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5254 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07800 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42400 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BICINE, PH 9.0, 1.6 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING 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 59.70900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.00700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.00700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.85450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.00700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.00700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.56350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.00700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.00700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.85450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.00700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.00700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.56350 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 59.70900 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE A 86 REMARK 465 ASN A 111 REMARK 465 GLY A 112 REMARK 465 SER A 113 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 THR A 26 120.02 -37.12 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 1MQ A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JV7 RELATED DB: PDB REMARK 900 RELATED ID: 4JV9 RELATED DB: PDB REMARK 900 RELATED ID: 4JVR RELATED DB: PDB REMARK 900 RELATED ID: 4JWR RELATED DB: PDB DBREF 4JVE A 18 111 UNP Q00987 MDM2_HUMAN 18 111 SEQADV 4JVE GLY A 112 UNP Q00987 EXPRESSION TAG SEQADV 4JVE SER A 113 UNP Q00987 EXPRESSION TAG SEQRES 1 A 96 GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG PRO SEQRES 2 A 96 LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY ALA SEQRES 3 A 96 GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE TYR SEQRES 4 A 96 LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP GLU SEQRES 5 A 96 LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU LEU SEQRES 6 A 96 GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS GLU SEQRES 7 A 96 HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU VAL SEQRES 8 A 96 VAL VAL ASN GLY SER HET 1MQ A 201 36 HETNAM 1MQ (2R,3E)-2-[(2S,3R,6S)-2,3-BIS(4-CHLOROPHENYL)-6-(4- HETNAM 2 1MQ FLUOROBENZYL)-5-OXOMORPHOLIN-4-YL]PENT-3-ENOIC ACID FORMUL 2 1MQ C28 H24 CL2 F N O4 FORMUL 3 HOH *40(H2 O) HELIX 1 1 PRO A 20 THR A 26 1 7 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 LEU A 85 1 6 HELIX 5 5 GLU A 95 ASN A 106 1 12 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 HIS A 73 ILE A 74 0 SHEET 2 B 2 PHE A 91 SER A 92 -1 O PHE A 91 N ILE A 74 SSBOND 1 CYS A 77 CYS A 77 1555 7646 2.68 SITE 1 AC1 10 ARG A 29 LEU A 54 PHE A 55 LEU A 57 SITE 2 AC1 10 GLY A 58 GLN A 59 MET A 62 ILE A 99 SITE 3 AC1 10 HOH A 314 HOH A 336 CRYST1 42.014 42.014 119.418 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 0.023802 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008374 0.00000