HEADER CHAPERONE/CHAPERONE INHIBITOR 21-JUL-11 3B27 TITLE HSP90 ALPHA N-TERMINAL DOMAIN IN COMPLEX WITH AN INHIBITOR RO4919127 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS CHAPERONE-CHAPERONE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.A.FUKAMI,N.ONO REVDAT 4 13-MAR-24 3B27 1 REMARK SEQADV REVDAT 3 11-OCT-17 3B27 1 REMARK REVDAT 2 19-JUN-13 3B27 1 JRNL REVDAT 1 14-SEP-11 3B27 0 JRNL AUTH T.MIURA,T.A.FUKAMI,K.HASEGAWA,N.ONO,A.SUDA,H.SHINDO, JRNL AUTH 2 D.O.YOON,S.J.KIM,Y.J.NA,Y.AOKI,N.SHIMMA,T.TSUKUDA, JRNL AUTH 3 Y.SHIRATORI JRNL TITL LEAD GENERATION OF HEAT SHOCK PROTEIN 90 INHIBITORS BY A JRNL TITL 2 COMBINATION OF FRAGMENT-BASED APPROACH, VIRTUAL SCREENING, JRNL TITL 3 AND STRUCTURE-BASED DRUG DESIGN JRNL REF BIOORG.MED.CHEM.LETT. V. 21 5778 2011 JRNL REFN ISSN 0960-894X JRNL PMID 21875802 JRNL DOI 10.1016/J.BMCL.2011.08.001 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 34246 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1723 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 : 17 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2114 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2196 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2012 REMARK 3 BIN R VALUE (WORKING SET) : 0.2193 REMARK 3 BIN FREE R VALUE : 0.2246 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.82 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 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 : 1691 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.70990 REMARK 3 B22 (A**2) : 3.61230 REMARK 3 B33 (A**2) : 0.09750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.40440 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.170 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.083 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.080 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.078 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.077 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1753 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2369 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 632 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 51 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 249 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1753 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 238 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2369 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.14 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.80 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.09 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3B27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000029985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.22200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21%(W/V) PEG3350, 0.3M MGCL2, 0.1M REMARK 280 TRIS-CL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 21.99800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 MET A 8 REMARK 465 ASP A 9 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 224 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 410 O HOH A 429 2.07 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 ALA A 166 -144.43 63.88 REMARK 500 ARG A 182 138.05 -172.47 REMARK 500 PHE A 213 59.15 -98.33 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 B2T A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B24 RELATED DB: PDB REMARK 900 RELATED ID: 3B25 RELATED DB: PDB REMARK 900 RELATED ID: 3B26 RELATED DB: PDB REMARK 900 RELATED ID: 3B28 RELATED DB: PDB DBREF 3B27 A 9 236 UNP P07900 HS90A_HUMAN 9 236 SEQADV 3B27 MET A 8 UNP P07900 EXPRESSION TAG SEQRES 1 A 229 MET ASP GLN PRO MET GLU GLU GLU GLU VAL GLU THR PHE SEQRES 2 A 229 ALA PHE GLN ALA GLU ILE ALA GLN LEU MET SER LEU ILE SEQRES 3 A 229 ILE ASN THR PHE TYR SER ASN LYS GLU ILE PHE LEU ARG SEQRES 4 A 229 GLU LEU ILE SER ASN SER SER ASP ALA LEU ASP LYS ILE SEQRES 5 A 229 ARG TYR GLU SER LEU THR ASP PRO SER LYS LEU ASP SER SEQRES 6 A 229 GLY LYS GLU LEU HIS ILE ASN LEU ILE PRO ASN LYS GLN SEQRES 7 A 229 ASP ARG THR LEU THR ILE VAL ASP THR GLY ILE GLY MET SEQRES 8 A 229 THR LYS ALA ASP LEU ILE ASN ASN LEU GLY THR ILE ALA SEQRES 9 A 229 LYS SER GLY THR LYS ALA PHE MET GLU ALA LEU GLN ALA SEQRES 10 A 229 GLY ALA ASP ILE SER MET ILE GLY GLN PHE GLY VAL GLY SEQRES 11 A 229 PHE TYR SER ALA TYR LEU VAL ALA GLU LYS VAL THR VAL SEQRES 12 A 229 ILE THR LYS HIS ASN ASP ASP GLU GLN TYR ALA TRP GLU SEQRES 13 A 229 SER SER ALA GLY GLY SER PHE THR VAL ARG THR ASP THR SEQRES 14 A 229 GLY GLU PRO MET GLY ARG GLY THR LYS VAL ILE LEU HIS SEQRES 15 A 229 LEU LYS GLU ASP GLN THR GLU TYR LEU GLU GLU ARG ARG SEQRES 16 A 229 ILE LYS GLU ILE VAL LYS LYS HIS SER GLN PHE ILE GLY SEQRES 17 A 229 TYR PRO ILE THR LEU PHE VAL GLU LYS GLU ARG ASP LYS SEQRES 18 A 229 GLU VAL SER ASP ASP GLU ALA GLU HET B2T A 1 16 HETNAM B2T 4-(2-CHLOROPHENYL)-6-(METHYLSULFANYL)-1,3,5-TRIAZIN-2- HETNAM 2 B2T AMINE FORMUL 2 B2T C10 H9 CL N4 S FORMUL 3 HOH *295(H2 O) HELIX 1 1 GLN A 23 THR A 36 1 14 HELIX 2 2 GLU A 42 ASP A 66 1 25 HELIX 3 3 PRO A 67 ASP A 71 5 5 HELIX 4 4 THR A 99 LEU A 107 1 9 HELIX 5 5 GLY A 114 ALA A 124 1 11 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 TYR A 160 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 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 12 ASN A 51 SER A 52 ALA A 55 ASP A 93 SITE 2 AC1 12 GLY A 97 MET A 98 LEU A 107 PHE A 138 SITE 3 AC1 12 THR A 184 HOH A 298 HOH A 303 HOH A 304 CRYST1 52.524 43.996 53.804 90.00 113.90 90.00 P 1 21 1 2 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 0.019039 0.000000 0.008437 0.00000 SCALE2 0.000000 0.022729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020329 0.00000