HEADER CHAPERONE 27-JUL-13 4LWH TITLE CRYSTAL STRUCTURE OF THE HUMAN HSP90-ALPHA N-DOMAIN BOUND TO THE HSP90 TITLE 2 INHIBITOR FJ5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 16-224; 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN FOLD, ATP BINDING, MOLECULARCHAPERONE, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,F.SHI,B.XIONG,J.HE REVDAT 3 08-NOV-23 4LWH 1 REMARK REVDAT 2 12-OCT-16 4LWH 1 JRNL REVDAT 1 30-JUL-14 4LWH 0 JRNL AUTH D.CHEN,A.SHEN,J.LI,F.SHI,W.CHEN,J.REN,H.LIU,Y.XU,X.WANG, JRNL AUTH 2 X.YANG,Y.SUN,M.YANG,J.HE,Y.WANG,L.ZHANG,M.HUANG,M.GENG, JRNL AUTH 3 B.XIONG,J.SHEN JRNL TITL DISCOVERY OF POTENT N-(ISOXAZOL-5-YL)AMIDES AS HSP90 JRNL TITL 2 INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 87 765 2014 JRNL REFN ISSN 0223-5234 JRNL PMID 25313505 JRNL DOI 10.1016/J.EJMECH.2014.09.065 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 32199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1965 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 33.2895 - 3.6617 0.97 3186 207 0.1739 0.1764 REMARK 3 2 3.6617 - 2.9069 1.00 3124 201 0.2026 0.2067 REMARK 3 3 2.9069 - 2.5396 1.00 3107 202 0.2121 0.2102 REMARK 3 4 2.5396 - 2.3075 0.99 3061 199 0.2028 0.2132 REMARK 3 5 2.3075 - 2.1421 0.99 3045 197 0.1923 0.2219 REMARK 3 6 2.1421 - 2.0158 0.99 3055 198 0.1874 0.2121 REMARK 3 7 2.0158 - 1.9149 0.98 3013 198 0.1861 0.2057 REMARK 3 8 1.9149 - 1.8316 0.96 2950 194 0.1875 0.2258 REMARK 3 9 1.8316 - 1.7610 0.94 2890 183 0.2116 0.2697 REMARK 3 10 1.7610 - 1.7003 0.92 2803 186 0.2212 0.2410 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.17 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 40.13 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.81120 REMARK 3 B22 (A**2) : 2.43240 REMARK 3 B33 (A**2) : -0.62120 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 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 : 0.006 1700 REMARK 3 ANGLE : 1.064 2296 REMARK 3 CHIRALITY : 0.075 258 REMARK 3 PLANARITY : 0.006 290 REMARK 3 DIHEDRAL : 17.577 642 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4LWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081172. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : 0.97913 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 33.283 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 37.5490 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 3T0Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% (W/V) PEG 2000 MONOMETHYL REMARK 280 ETHER, 200MM MAGNESIUM CHLORIDE, 100MM SODIUM CACODYLATE PH 6.5,, REMARK 280 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 33.20850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.66700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.90650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.20850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.66700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.90650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.20850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.66700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.90650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.20850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.66700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.90650 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 LYS A 224 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 41.70 -106.50 REMARK 500 ALA A 166 -145.37 66.09 REMARK 500 ARG A 182 139.71 -171.51 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 FJ5 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LWE RELATED DB: PDB REMARK 900 RELATED ID: 4LWF RELATED DB: PDB REMARK 900 RELATED ID: 4LWG RELATED DB: PDB REMARK 900 RELATED ID: 4LWI RELATED DB: PDB DBREF 4LWH A 16 224 UNP P07900 HS90A_HUMAN 16 224 SEQRES 1 A 209 GLU VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN SEQRES 2 A 209 LEU MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS SEQRES 3 A 209 GLU ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP SEQRES 4 A 209 ALA LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP PRO SEQRES 5 A 209 SER LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU SEQRES 6 A 209 ILE PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP SEQRES 7 A 209 THR GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN SEQRES 8 A 209 LEU GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET SEQRES 9 A 209 GLU ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY SEQRES 10 A 209 GLN PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA SEQRES 11 A 209 GLU LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU SEQRES 12 A 209 GLN TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR SEQRES 13 A 209 VAL ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR SEQRES 14 A 209 LYS VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR SEQRES 15 A 209 LEU GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS SEQRES 16 A 209 SER GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU SEQRES 17 A 209 LYS HET FJ5 A 301 35 HETNAM FJ5 N-{3-[2,4-DIHYDROXY-5-(PROPAN-2-YL)PHENYL]-4-[4- HETNAM 2 FJ5 (MORPHOLIN-4-YLMETHYL)PHENYL]-1,2-OXAZOL-5- HETNAM 3 FJ5 YL}CYCLOPROPANECARBOXAMIDE FORMUL 2 FJ5 C27 H31 N3 O5 FORMUL 3 HOH *118(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 ILE A 110 ALA A 124 1 15 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 16 ASN A 51 ASP A 54 ALA A 55 LYS A 58 SITE 2 AC1 16 ASP A 93 ILE A 96 GLY A 97 MET A 98 SITE 3 AC1 16 LEU A 107 THR A 109 PHE A 138 THR A 184 SITE 4 AC1 16 VAL A 186 HOH A 401 HOH A 402 HOH A 427 CRYST1 66.417 89.334 99.813 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 0.015056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010019 0.00000