PDB Short entry for 4LWI HEADER CHAPERONE 27-JUL-13 4LWI TITLE CRYSTAL STRUCTURE OF THE HUMAN HSP90-ALPHA N-DOMAIN BOUND TO THE HSP90 TITLE 2 INHIBITOR FJ6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 17-224; 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 4LWI 1 REMARK REVDAT 2 12-OCT-16 4LWI 1 JRNL REVDAT 1 30-JUL-14 4LWI 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: 1.8.1_1168) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 31624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.320 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 34.6224 - 4.0960 0.99 2294 154 0.1692 0.1826 REMARK 3 2 4.0960 - 3.2519 1.00 2214 150 0.1786 0.2080 REMARK 3 3 3.2519 - 2.8410 0.99 2177 147 0.2131 0.2124 REMARK 3 4 2.8410 - 2.5814 0.99 2180 148 0.2175 0.2586 REMARK 3 5 2.5814 - 2.3964 0.99 2153 145 0.2127 0.2204 REMARK 3 6 2.3964 - 2.2551 0.99 2142 144 0.1998 0.2449 REMARK 3 7 2.2551 - 2.1422 0.99 2159 146 0.1858 0.2288 REMARK 3 8 2.1422 - 2.0490 0.98 2125 144 0.1949 0.1855 REMARK 3 9 2.0490 - 1.9701 0.98 2102 142 0.1879 0.2164 REMARK 3 10 1.9701 - 1.9021 0.97 2094 141 0.1851 0.2433 REMARK 3 11 1.9021 - 1.8426 0.95 2073 140 0.1849 0.1921 REMARK 3 12 1.8426 - 1.7900 0.95 2028 137 0.1892 0.2054 REMARK 3 13 1.7900 - 1.7429 0.92 1988 135 0.1901 0.2446 REMARK 3 14 1.7429 - 1.7003 0.89 1895 127 0.1934 0.2291 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.310 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1685 REMARK 3 ANGLE : 1.113 2276 REMARK 3 CHIRALITY : 0.075 257 REMARK 3 PLANARITY : 0.004 289 REMARK 3 DIHEDRAL : 14.942 630 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 4LWI 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_1000081173. 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 : NULL 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 : 0.97923 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 : 32571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 34.615 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 48.2730 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 <I/SIGMA(I)> 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 (%): 60.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 32.83300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.62800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.85750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.83300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.62800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.85750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.83300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.62800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.85750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.83300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.62800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.85750 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 40.55 -109.02 REMARK 500 ILE A 110 58.13 -90.76 REMARK 500 ALA A 166 -145.23 64.72 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 FJ6 A 301 DBREF 4LWI A 17 224 UNP P07900 HS90A_HUMAN 17 224 SEQRES 1 A 208 VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA GLN LEU SEQRES 2 A 208 MET SER LEU ILE ILE ASN THR PHE TYR SER ASN LYS GLU SEQRES 3 A 208 ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER ASP ALA SEQRES 4 A 208 LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP PRO SER SEQRES 5 A 208 LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN LEU ILE SEQRES 6 A 208 PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL ASP THR SEQRES 7 A 208 GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN ASN LEU SEQRES 8 A 208 GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE MET GLU SEQRES 9 A 208 ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE GLY GLN SEQRES 10 A 208 PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL ALA GLU SEQRES 11 A 208 LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP GLU GLN SEQRES 12 A 208 TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE THR VAL SEQRES 13 A 208 ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY THR LYS SEQRES 14 A 208 VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU TYR LEU SEQRES 15 A 208 GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS HIS SER SEQRES 16 A 208 GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL GLU LYS HET FJ6 A 301 30 HETNAM FJ6 N-{3-[2,4-DIHYDROXY-5-(PROPAN-2-YL)PHENYL]-4-(4- HETNAM 2 FJ6 METHOXYPHENYL)-1,2-OXAZOL-5-YL}CYCLOPROPANECARBOXAMIDE FORMUL 2 FJ6 C23 H24 N2 O5 FORMUL 3 HOH *110(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 ASN A 105 1 7 HELIX 5 5 ASN A 106 THR A 109 5 4 HELIX 6 6 ILE A 110 GLU A 120 1 11 HELIX 7 7 ASP A 127 GLY A 135 5 9 HELIX 8 8 VAL A 136 LEU A 143 5 8 HELIX 9 9 GLU A 192 LEU A 198 5 7 HELIX 10 10 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 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 18 LEU A 48 ASN A 51 ASP A 54 ALA A 55 SITE 2 AC1 18 LYS A 58 ASP A 93 ILE A 96 GLY A 97 SITE 3 AC1 18 MET A 98 LEU A 107 GLY A 108 PHE A 138 SITE 4 AC1 18 THR A 184 VAL A 186 HOH A 402 HOH A 403 SITE 5 AC1 18 HOH A 431 HOH A 443 CRYST1 65.666 89.256 99.715 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 0.015229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010029 0.00000