HEADER CHAPERONE 28-JUN-07 2QG2 TITLE HSP90 COMPLEXED WITH A917985 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSP 86, RENAL CARCINOMA ANTIGEN NY-REN-38; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: HSP90AA1, HSP90A, HSPC1, HSPCA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS PROTEIN-INHIBITOR COMPLEX, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR C.H.PARK REVDAT 3 30-AUG-23 2QG2 1 REMARK SEQADV REVDAT 2 24-FEB-09 2QG2 1 VERSN REVDAT 1 01-JUL-08 2QG2 0 JRNL AUTH J.R.HUTH,C.PARK,A.M.PETROS,A.R.KUNZER,M.D.WENDT,X.WANG, JRNL AUTH 2 C.L.LYNCH,J.C.MACK,K.M.SWIFT,R.A.JUDGE,J.CHEN, JRNL AUTH 3 P.L.RICHARDSON,S.JIN,S.K.TAHIR,E.D.MATAYOSHI,S.A.DORWIN, JRNL AUTH 4 U.S.LADROR,J.M.SEVERIN,K.A.WALTER,D.M.BARTLEY,S.W.FESIK, JRNL AUTH 5 S.W.ELMORE,P.J.HAJDUK JRNL TITL DISCOVERY AND DESIGN OF NOVEL HSP90 INHIBITORS USING JRNL TITL 2 MULTIPLE FRAGMENT-BASED DESIGN STRATEGIES. JRNL REF CHEM.BIOL.DRUG DES. V. 70 1 2007 JRNL REFN ISSN 1747-0277 JRNL PMID 17630989 JRNL DOI 10.1111/J.1747-0285.2007.00535.X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2002 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 194499.880 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.4 REMARK 3 NUMBER OF REFLECTIONS : 23007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2279 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 28225 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 31.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 768 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 90 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1628 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.48000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : 6.17000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.540 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.490 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.320 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 59.78 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 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : ACCELRYS_CNX_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ACCELRYS_CNX_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : A91.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : A91.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2QG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24541 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37200 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1YER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MG/ML PROTEIN WITH A RESERVOIR REMARK 280 SOLUTION OF 8-18 %(W/V) PMME 2000, 0.1 M SODIUM CACODYLATE PH REMARK 280 6.5, 0.2 M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.39600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.69150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.16950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.39600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.69150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.16950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.39600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.69150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.16950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.39600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.69150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.16950 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 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 94 42.38 -108.78 REMARK 500 ASN A 105 -51.41 -128.43 REMARK 500 ALA A 166 -138.15 68.55 REMARK 500 ARG A 182 137.22 -170.15 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 A91 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QF6 RELATED DB: PDB REMARK 900 RELATED ID: 2QFO RELATED DB: PDB REMARK 900 RELATED ID: 2QG0 RELATED DB: PDB DBREF 2QG2 A 17 223 UNP P07900 HS90A_HUMAN 17 223 SEQADV 2QG2 THR A 63 UNP P07900 SER 63 CONFLICT SEQRES 1 A 207 VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN LEU SEQRES 2 A 207 MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS GLU SEQRES 3 A 207 ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP ALA SEQRES 4 A 207 LEU ASP LYS ILE ARG TYR GLU THR LEU THR ASP PRO SER SEQRES 5 A 207 LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU ILE SEQRES 6 A 207 PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP THR SEQRES 7 A 207 GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN LEU SEQRES 8 A 207 GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET GLU SEQRES 9 A 207 ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY GLN SEQRES 10 A 207 PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA GLU SEQRES 11 A 207 LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU GLN SEQRES 12 A 207 TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR VAL SEQRES 13 A 207 ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR LYS SEQRES 14 A 207 VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR LEU SEQRES 15 A 207 GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS SER SEQRES 16 A 207 GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU HET A91 A 300 24 HETNAM A91 3-({2-[(2-AMINO-6-METHYLPYRIMIDIN-4-YL) HETNAM 2 A91 ETHYNYL]BENZYL}AMINO)-1,3-OXAZOL-2(3H)-ONE FORMUL 2 A91 C17 H15 N5 O2 FORMUL 3 HOH *267(H2 O) HELIX 1 1 GLN A 23 THR A 36 1 14 HELIX 2 2 GLU A 42 LEU A 64 1 23 HELIX 3 3 THR A 65 ASP A 71 5 7 HELIX 4 4 THR A 99 ASN A 105 1 7 HELIX 5 5 ASN A 105 ALA A 124 1 20 HELIX 6 6 ASP A 127 GLY A 135 5 9 HELIX 7 7 VAL A 136 LEU A 143 5 8 HELIX 8 8 GLN A 194 LEU A 198 5 5 HELIX 9 9 GLU A 199 SER A 211 1 13 SHEET 1 A 8 GLU A 18 ALA A 21 0 SHEET 2 A 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 A 8 GLN A 159 SER A 164 -1 N GLU A 163 O THR A 171 SHEET 4 A 8 ALA A 145 LYS A 153 -1 N VAL A 150 O TRP A 162 SHEET 5 A 8 GLY A 183 LEU A 190 -1 O ILE A 187 N THR A 149 SHEET 6 A 8 THR A 88 ASP A 93 -1 N ILE A 91 O VAL A 186 SHEET 7 A 8 ILE A 78 ASN A 83 -1 N ASN A 79 O VAL A 92 SHEET 8 A 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 16 ASN A 51 ALA A 55 ASP A 93 ILE A 96 SITE 2 AC1 16 GLY A 97 LEU A 103 LEU A 107 GLY A 135 SITE 3 AC1 16 PHE A 138 TYR A 139 TRP A 162 THR A 184 SITE 4 AC1 16 HOH A 302 HOH A 306 HOH A 308 HOH A 560 CRYST1 66.792 91.383 98.339 90.00 90.00 90.00 I 2 2 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 0.014972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010943 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010169 0.00000