HEADER CHAPERONE/CHAPERONE INHIBITOR 13-DEC-13 4O04 TITLE IDENTIFICATION OF NOVEL HSP90/ISOFORM SELECTIVE INHIBITORS USING TITLE 2 STRUCTURE-BASED DRUG DESIGN. DEMONSTRATION OF POTENTIAL UTILITY IN TITLE 3 TREATING CNS DISORDERS SUCH AS HUNTINGTON'S DISEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 9-236; COMPND 5 SYNONYM: HEAT SHOCK 86 KDA, HSP 86, HSP86, RENAL CARCINOMA ANTIGEN COMPND 6 NY-REN-38; COMPND 7 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: HSP90AA1, HSP90A, HSPC1, HSPCA; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CHAPERONE, CHAPERONE-CHAPERONE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.J.ZUCCOLA,J.ERNST REVDAT 3 28-FEB-24 4O04 1 REMARK SEQADV REVDAT 2 22-NOV-17 4O04 1 REMARK REVDAT 1 24-DEC-14 4O04 0 JRNL AUTH J.T.ERNST,T.NEUBERT,M.LIU,S.SPERRY,H.ZUCCOLA,A.TURNBULL, JRNL AUTH 2 B.FLECK,W.KARGO,L.WOODY,P.CHIANG,D.TRAN,W.CHEN,P.SNYDER, JRNL AUTH 3 T.ALCACIO,A.NEZAMI,J.REYNOLDS,K.ALVI,L.GOULET,D.STAMOS JRNL TITL IDENTIFICATION OF NOVEL HSP90 ALPHA / BETA ISOFORM SELECTIVE JRNL TITL 2 INHIBITORS USING STRUCTURE-BASED DRUG DESIGN. DEMONSTRATION JRNL TITL 3 OF POTENTIAL UTILITY IN TREATING CNS DISORDERS SUCH AS JRNL TITL 4 HUNTINGTON'S DISEASE. JRNL REF J.MED.CHEM. V. 57 3382 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 24673104 JRNL DOI 10.1021/JM500042S REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 26686 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1340 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1913 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 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1635 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 21.530 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; 2.000 ; 0 REMARK 3 BOND ANGLES (DEGREES) : NULL ; 5.000 ; 1 REMARK 3 TORSION ANGLES (DEGREES) : NULL ; 2.000 ; 14 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4O04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.816 REMARK 200 RESOLUTION RANGE LOW (A) : 66.982 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 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) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: DIFFERENCE FOURIER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25%PEGMME2K, 0.2M MGCL2,0.1M REMARK 280 CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 33.59500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.46000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.53000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.59500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.46000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.53000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.59500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.46000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.53000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.59500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.46000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.53000 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 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 GLY A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 REMARK 465 HIS A 7 REMARK 465 MET A 8 REMARK 465 ASP A 9 REMARK 465 GLN A 10 REMARK 465 PRO A 11 REMARK 465 MET A 12 REMARK 465 GLU A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 LYS A 224 REMARK 465 GLU A 225 REMARK 465 ARG A 226 REMARK 465 ASP A 227 REMARK 465 LYS A 228 REMARK 465 GLU A 229 REMARK 465 VAL A 230 REMARK 465 SER A 231 REMARK 465 ASP A 232 REMARK 465 ASP A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 GLU A 236 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 ASN A 105 -51.03 -120.81 REMARK 500 ALA A 166 -144.62 67.87 REMARK 500 ARG A 182 142.05 -171.83 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 2Q8 A 4000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O05 RELATED DB: PDB REMARK 900 RELATED ID: 4O06 RELATED DB: PDB REMARK 900 RELATED ID: 4O09 RELATED DB: PDB REMARK 900 RELATED ID: 4O0B RELATED DB: PDB DBREF 4O04 A 9 236 UNP P07900 HS90A_HUMAN 9 236 SEQADV 4O04 GLY A 4 UNP P07900 EXPRESSION TAG SEQADV 4O04 SER A 5 UNP P07900 EXPRESSION TAG SEQADV 4O04 LEU A 6 UNP P07900 EXPRESSION TAG SEQADV 4O04 HIS A 7 UNP P07900 EXPRESSION TAG SEQADV 4O04 MET A 8 UNP P07900 EXPRESSION TAG SEQRES 1 A 233 GLY SER LEU HIS MET ASP GLN PRO MET GLU GLU GLU GLU SEQRES 2 A 233 VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN LEU SEQRES 3 A 233 MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS GLU SEQRES 4 A 233 ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP ALA SEQRES 5 A 233 LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP PRO SER SEQRES 6 A 233 LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU ILE SEQRES 7 A 233 PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP THR SEQRES 8 A 233 GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN LEU SEQRES 9 A 233 GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET GLU SEQRES 10 A 233 ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY GLN SEQRES 11 A 233 PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA GLU SEQRES 12 A 233 LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU GLN SEQRES 13 A 233 TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR VAL SEQRES 14 A 233 ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR LYS SEQRES 15 A 233 VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR LEU SEQRES 16 A 233 GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS SER SEQRES 17 A 233 GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU LYS SEQRES 18 A 233 GLU ARG ASP LYS GLU VAL SER ASP ASP GLU ALA GLU HET 2Q8 A4000 26 HETNAM 2Q8 4-(2,7,7-TRIMETHYL-5-OXO-1,2,3,4,5,6,7,8-OCTAHYDRO-9H- HETNAM 2 2Q8 BETA-CARBOLIN-9-YL)BENZAMIDE FORMUL 2 2Q8 C21 H25 N3 O2 FORMUL 3 HOH *202(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 GLU A 192 LEU A 198 5 7 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 ALA A 161 O ARG A 173 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 LEU A 89 O LEU A 188 SHEET 7 A 8 ILE A 78 ASN A 83 -1 N ILE A 81 O THR A 90 SHEET 8 A 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 10 ALA A 55 ASP A 93 GLY A 135 TYR A 139 SITE 2 AC1 10 TRP A 162 THR A 184 HOH A4108 HOH A4112 SITE 3 AC1 10 HOH A4124 HOH A4195 CRYST1 67.190 90.920 99.060 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 0.014883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010095 0.00000