HEADER HYDROLASE/HYDROLASE INHIBITOR 07-OCT-09 3K5D TITLE CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH AHM178 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA- COMPND 6 SITE APP CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, COMPND 7 MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; COMPND 8 EC: 3.4.23.46; COMPND 9 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: BACE, BACE1, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 TUNER (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24 KEYWDS ASPARTYL PROTEASE, ALZHEIMER'S DISEASE, ENDOPLASMIC RETICULUM, KEYWDS 2 ENDOSOME, GLYCOPROTEIN, GOLGI APPARATUS, MEMBRANE, PROTEASE, KEYWDS 3 TRANSMEMBRANE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.-M.RONDEAU REVDAT 4 06-NOV-24 3K5D 1 REMARK REVDAT 3 01-NOV-17 3K5D 1 REMARK REVDAT 2 13-JUL-11 3K5D 1 VERSN REVDAT 1 05-MAY-10 3K5D 0 JRNL AUTH S.HANESSIAN,Z.SHAO,C.BETSCHART,J.M.RONDEAU,U.NEUMANN, JRNL AUTH 2 M.TINTELNOT-BLOMLEY JRNL TITL STRUCTURE-BASED DESIGN AND SYNTHESIS OF NOVEL P2/P3 JRNL TITL 2 MODIFIED, NON-PEPTIDIC BETA-SECRETASE (BACE-1) INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 1924 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20172717 JRNL DOI 10.1016/J.BMCL.2010.01.139 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.MACHAUER,S.VEENSTRA,J.-M.RONDEAU,M.TINTELNOT-BLOMLEY, REMARK 1 AUTH 2 C.BETSCHART,P.PAGANETTI,U.NEUMANN REMARK 1 TITL STRUCTURE-BASED DESIGN AND SYNTHESIS OF MACROCYCLIC REMARK 1 TITL 2 PEPTIDOMIMETIC BETA-SECRETASE (BACE-1) INHIBITORS REMARK 1 REF BIOORG. MED. CHEM. LETT. V. 19 1361 2009 REMARK 1 REFN ISSN 0960-894X REMARK 1 REFERENCE 2 REMARK 1 AUTH R.MACHAUER,K.LAUMEN,S.VEENSTRA,J.-M.RONDEAU, REMARK 1 AUTH 2 M.TINTELNOT-BLOMLEY,C.BETSCHART,A.-L.JATON,S.DESRAYAUD, REMARK 1 AUTH 3 M.STAUFENBIEL,S.RABE,P.PAGANETTI,U.NEUMANN REMARK 1 TITL MACROCYCLIC PEPTIDOMIMETIC BETA-SECRETASE (BACE-1) REMARK 1 TITL 2 INHIBITORS WITH ACTIVITY IN VIVO REMARK 1 REF BIOORG. MED. CHEM. LETT. V. 19 1366 2009 REMARK 1 REFN ISSN 0960-894X REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 13448246.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 36217 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3615 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 36242 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5291 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 604 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8867 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 111 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.85000 REMARK 3 B22 (A**2) : 4.32000 REMARK 3 B33 (A**2) : 2.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 3.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.630 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.080 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 36.69 REMARK 3 REMARK 3 NCS MODEL : NONE 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 : WATER_REP.PAR REMARK 3 PARAMETER FILE 4 : NVP-AHM178.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 3 : NVP-AHM178.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000055566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98030 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36226 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.10900 REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : 0.48000 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: CNX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN FROM 12% (W/V) PEG REMARK 280 8,000, 0.1M KCL, 5% GLYCEROL. PROTEIN STOCK WAS 12.7MG/ML BACE REMARK 280 IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 2-FOLD EXCESS OF REMARK 280 COMPOUND ADDED FROM A 50MM STOCK SOLUTION IN DMSO (0.55% DMSO IN REMARK 280 DROP). BEFORE MOUNTING, THE CRYSTALS WERE BRIEFLY TRANSFERRED TO REMARK 280 A CRYO-PROTECTANT SOLUTION CONTAINING 12% (W/V) PEG 8,000, 0.5M REMARK 280 KCL, 15% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292K, PH 5.5 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 50.64950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER. THERE ARE 3 BIOLOGICAL REMARK 300 UNITS IN THE ASYMMETRIC UNIT (CHAINS A, B AND C) 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 33P REMARK 465 PRO A 34P REMARK 465 ASP A 35P REMARK 465 GLU A 36P REMARK 465 GLU A 37P REMARK 465 PRO A 38P REMARK 465 GLU A 39P REMARK 465 GLU A 40P REMARK 465 PRO A 41P REMARK 465 GLY A 42P REMARK 465 ARG A 43P REMARK 465 ARG A 44P REMARK 465 GLY A 45P REMARK 465 GLY A 158 REMARK 465 PHE A 159 REMARK 465 PRO A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 LEU A 167 REMARK 465 ALA A 168 REMARK 465 SER A 169 REMARK 465 VAL A 170 REMARK 465 ILE A 386 REMARK 465 PRO A 387 REMARK 465 GLN A 388 REMARK 465 THR A 389 REMARK 465 ASP A 390 REMARK 465 GLU A 391 REMARK 465 SER A 392 REMARK 465 GLY B 33P REMARK 465 PRO B 34P REMARK 465 ASP B 35P REMARK 465 GLU B 36P REMARK 465 GLU B 37P REMARK 465 PRO B 38P REMARK 465 GLU B 39P REMARK 465 GLU B 40P REMARK 465 PRO B 41P REMARK 465 GLY B 42P REMARK 465 ARG B 43P REMARK 465 ARG B 44P REMARK 465 GLY B 45P REMARK 465 GLY B 158 REMARK 465 PHE B 159 REMARK 465 PRO B 160 REMARK 465 LEU B 161 REMARK 465 ASN B 162 REMARK 465 GLN B 163 REMARK 465 SER B 164 REMARK 465 GLU B 165 REMARK 465 VAL B 166 REMARK 465 LEU B 167 REMARK 465 ALA B 168 REMARK 465 SER B 169 REMARK 465 VAL B 170 REMARK 465 ILE B 386 REMARK 465 PRO B 387 REMARK 465 GLN B 388 REMARK 465 THR B 389 REMARK 465 ASP B 390 REMARK 465 GLU B 391 REMARK 465 SER B 392 REMARK 465 GLY C 33P REMARK 465 PRO C 34P REMARK 465 ASP C 35P REMARK 465 GLU C 36P REMARK 465 GLU C 37P REMARK 465 PRO C 38P REMARK 465 GLU C 39P REMARK 465 GLU C 40P REMARK 465 PRO C 41P REMARK 465 GLY C 42P REMARK 465 ARG C 43P REMARK 465 ARG C 44P REMARK 465 GLY C 45P REMARK 465 GLY C 158 REMARK 465 PHE C 159 REMARK 465 PRO C 160 REMARK 465 LEU C 161 REMARK 465 ASN C 162 REMARK 465 GLN C 163 REMARK 465 SER C 164 REMARK 465 GLU C 165 REMARK 465 VAL C 166 REMARK 465 LEU C 167 REMARK 465 ALA C 168 REMARK 465 SER C 169 REMARK 465 VAL C 170 REMARK 465 PRO C 387 REMARK 465 GLN C 388 REMARK 465 THR C 389 REMARK 465 ASP C 390 REMARK 465 GLU C 391 REMARK 465 SER C 392 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 PHE A 108 -66.64 -106.05 REMARK 500 ASN A 114 -4.58 82.26 REMARK 500 ASP A 131 9.61 -67.44 REMARK 500 THR A 144 -165.00 -124.72 REMARK 500 LEU A 149 137.69 -175.89 REMARK 500 TRP A 197 -70.79 -140.74 REMARK 500 ARG A 205 143.80 -170.23 REMARK 500 LYS A 214 74.86 40.81 REMARK 500 TYR A 222 105.18 -58.50 REMARK 500 ASP A 223 -70.73 94.72 REMARK 500 TRP A 262 0.26 -69.98 REMARK 500 GLU A 265 -70.43 -79.47 REMARK 500 SER A 315 -163.32 -126.78 REMARK 500 HIS A 362 137.69 177.05 REMARK 500 PHE A 365 -54.12 -132.95 REMARK 500 ASP B 4 38.75 74.14 REMARK 500 PHE B 108 -67.04 -106.04 REMARK 500 ASN B 114 -4.90 82.19 REMARK 500 ASP B 131 9.38 -67.86 REMARK 500 THR B 144 -165.66 -125.23 REMARK 500 LEU B 149 137.22 -175.40 REMARK 500 TRP B 197 -70.83 -139.86 REMARK 500 ARG B 205 139.87 -177.25 REMARK 500 LYS B 214 75.30 43.03 REMARK 500 ASP B 223 -70.75 90.41 REMARK 500 GLU B 265 -70.02 -78.97 REMARK 500 GLN B 294 52.27 -150.75 REMARK 500 SER B 315 -163.33 -126.86 REMARK 500 PHE B 365 -53.97 -132.68 REMARK 500 GLU B 380 0.86 -63.90 REMARK 500 PHE C 108 -67.23 -105.71 REMARK 500 ASN C 114 -6.02 82.72 REMARK 500 ASP C 131 8.90 -67.96 REMARK 500 THR C 144 -165.18 -125.17 REMARK 500 LEU C 149 138.25 -175.44 REMARK 500 TRP C 197 -71.28 -140.51 REMARK 500 ARG C 205 151.05 176.54 REMARK 500 LYS C 214 76.77 41.50 REMARK 500 ASP C 223 -70.59 89.88 REMARK 500 GLU C 265 -70.00 -79.07 REMARK 500 SER C 315 -163.43 -126.60 REMARK 500 PHE C 365 -54.66 -133.11 REMARK 500 ASP C 381 4.20 -68.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR XLI INCORPORATES A HYDROXYETHYLENE ISOSTERE REMARK 600 IN THE PEPTIDE BACKBONE REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE ENZYME INHIBITOR REMARK 630 MOLECULE NAME: N-ACETYL-L-LEUCYL-N-[(4S,5S,7R)-8-(BUTYLAMINO)-5- REMARK 630 HYDROXY-2,7-DIMETHYL-8-OXOOCTAN-4-YL]-L-METHIONINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 XLI A 393 REMARK 630 XLI B 393 REMARK 630 XLI C 393 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACE LEU MET 1OL LYT REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XLI A 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XLI B 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XLI C 393 DBREF 3K5D A 35P 392 UNP P56817 BACE1_HUMAN 48 453 DBREF 3K5D B 35P 392 UNP P56817 BACE1_HUMAN 48 453 DBREF 3K5D C 35P 392 UNP P56817 BACE1_HUMAN 48 453 SEQADV 3K5D GLY A 33P UNP P56817 EXPRESSION TAG SEQADV 3K5D PRO A 34P UNP P56817 EXPRESSION TAG SEQADV 3K5D GLY B 33P UNP P56817 EXPRESSION TAG SEQADV 3K5D PRO B 34P UNP P56817 EXPRESSION TAG SEQADV 3K5D GLY C 33P UNP P56817 EXPRESSION TAG SEQADV 3K5D PRO C 34P UNP P56817 EXPRESSION TAG SEQRES 1 A 408 GLY PRO ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SEQRES 2 A 408 SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER SEQRES 3 A 408 GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO SEQRES 4 A 408 PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SER SEQRES 5 A 408 ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS SEQRES 6 A 408 ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP SEQRES 7 A 408 LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS SEQRES 8 A 408 TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO SEQRES 9 A 408 HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA SEQRES 10 A 408 ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN SEQRES 11 A 408 TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA SEQRES 12 A 408 ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU SEQRES 13 A 408 VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN SEQRES 14 A 408 LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL SEQRES 15 A 408 LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE SEQRES 16 A 408 ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR PRO SEQRES 17 A 408 ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG SEQRES 18 A 408 VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS SEQRES 19 A 408 GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR SEQRES 20 A 408 THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA SEQRES 21 A 408 VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS PHE SEQRES 22 A 408 PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP SEQRES 23 A 408 GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SEQRES 24 A 408 SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE SEQRES 25 A 408 ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL SEQRES 26 A 408 GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE SEQRES 27 A 408 ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY ALA SEQRES 28 A 408 VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA SEQRES 29 A 408 ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL SEQRES 30 A 408 HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE SEQRES 31 A 408 VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO SEQRES 32 A 408 GLN THR ASP GLU SER SEQRES 1 B 408 GLY PRO ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SEQRES 2 B 408 SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER SEQRES 3 B 408 GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO SEQRES 4 B 408 PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SER SEQRES 5 B 408 ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS SEQRES 6 B 408 ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP SEQRES 7 B 408 LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS SEQRES 8 B 408 TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO SEQRES 9 B 408 HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA SEQRES 10 B 408 ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN SEQRES 11 B 408 TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA SEQRES 12 B 408 ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU SEQRES 13 B 408 VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN SEQRES 14 B 408 LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL SEQRES 15 B 408 LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE SEQRES 16 B 408 ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR PRO SEQRES 17 B 408 ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG SEQRES 18 B 408 VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS SEQRES 19 B 408 GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR SEQRES 20 B 408 THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA SEQRES 21 B 408 VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS PHE SEQRES 22 B 408 PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP SEQRES 23 B 408 GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SEQRES 24 B 408 SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE SEQRES 25 B 408 ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL SEQRES 26 B 408 GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE SEQRES 27 B 408 ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY ALA SEQRES 28 B 408 VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA SEQRES 29 B 408 ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL SEQRES 30 B 408 HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE SEQRES 31 B 408 VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO SEQRES 32 B 408 GLN THR ASP GLU SER SEQRES 1 C 408 GLY PRO ASP GLU GLU PRO GLU GLU PRO GLY ARG ARG GLY SEQRES 2 C 408 SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER SEQRES 3 C 408 GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO SEQRES 4 C 408 PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SER SEQRES 5 C 408 ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS SEQRES 6 C 408 ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP SEQRES 7 C 408 LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS SEQRES 8 C 408 TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO SEQRES 9 C 408 HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA SEQRES 10 C 408 ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN SEQRES 11 C 408 TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA SEQRES 12 C 408 ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU SEQRES 13 C 408 VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN SEQRES 14 C 408 LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL SEQRES 15 C 408 LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE SEQRES 16 C 408 ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR PRO SEQRES 17 C 408 ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG SEQRES 18 C 408 VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS SEQRES 19 C 408 GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR SEQRES 20 C 408 THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA SEQRES 21 C 408 VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS PHE SEQRES 22 C 408 PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP SEQRES 23 C 408 GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SEQRES 24 C 408 SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE SEQRES 25 C 408 ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL SEQRES 26 C 408 GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE SEQRES 27 C 408 ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY ALA SEQRES 28 C 408 VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA SEQRES 29 C 408 ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL SEQRES 30 C 408 HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE SEQRES 31 C 408 VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO SEQRES 32 C 408 GLN THR ASP GLU SER HET XLI A 393 37 HET XLI B 393 37 HET XLI C 393 37 HETNAM XLI N-ACETYL-L-LEUCYL-N-[(4S,5S,7R)-8-(BUTYLAMINO)-5- HETNAM 2 XLI HYDROXY-2,7-DIMETHYL-8-OXOOCTAN-4-YL]-L-METHIONINAMIDE FORMUL 4 XLI 3(C27 H52 N4 O5 S) FORMUL 7 HOH *71(H2 O) HELIX 1 1 PHE A 47P VAL A 3 5 5 HELIX 2 2 GLN A 53 SER A 57 5 5 HELIX 3 3 TYR A 123 ALA A 127 5 5 HELIX 4 4 PRO A 135 THR A 144 1 10 HELIX 5 5 ASP A 180 TYR A 184 5 5 HELIX 6 6 ASP A 216 ASN A 221 1 6 HELIX 7 7 LYS A 238 SER A 252 1 15 HELIX 8 8 PRO A 276 PHE A 280 5 5 HELIX 9 9 LEU A 301 TYR A 305 1 5 HELIX 10 10 GLY A 334 GLY A 340 1 7 HELIX 11 11 ARG A 347 ARG A 349 5 3 HELIX 12 12 MET A 379 GLY A 383 5 5 HELIX 13 13 SER B 46P MET B 2 5 5 HELIX 14 14 GLN B 53 SER B 57 5 5 HELIX 15 15 TYR B 123 ALA B 127 5 5 HELIX 16 16 PRO B 135 THR B 144 1 10 HELIX 17 17 ASP B 180 TYR B 184 5 5 HELIX 18 18 ASP B 216 ASN B 221 1 6 HELIX 19 19 LYS B 238 SER B 252 1 15 HELIX 20 20 PRO B 276 PHE B 280 5 5 HELIX 21 21 VAL B 291 GLN B 294 5 4 HELIX 22 22 LEU B 301 TYR B 305 1 5 HELIX 23 23 GLY B 334 GLY B 340 1 7 HELIX 24 24 ARG B 347 ARG B 349 5 3 HELIX 25 25 ASP B 378 GLY B 383 1 6 HELIX 26 26 PHE C 47P VAL C 3 5 5 HELIX 27 27 GLN C 53 SER C 57 5 5 HELIX 28 28 TYR C 123 ALA C 127 5 5 HELIX 29 29 PRO C 135 THR C 144 1 10 HELIX 30 30 ASP C 180 TYR C 184 5 5 HELIX 31 31 ASP C 216 ASN C 221 1 6 HELIX 32 32 LYS C 238 SER C 252 1 15 HELIX 33 33 PRO C 276 PHE C 280 5 5 HELIX 34 34 LEU C 301 TYR C 305 1 5 HELIX 35 35 GLY C 334 GLU C 339 1 6 HELIX 36 36 ARG C 347 ARG C 349 5 3 HELIX 37 37 MET C 379 GLY C 383 5 5 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.03 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.04 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.04 SSBOND 4 CYS B 155 CYS B 359 1555 1555 2.04 SSBOND 5 CYS B 217 CYS B 382 1555 1555 2.04 SSBOND 6 CYS B 269 CYS B 319 1555 1555 2.04 SSBOND 7 CYS C 155 CYS C 359 1555 1555 2.04 SSBOND 8 CYS C 217 CYS C 382 1555 1555 2.04 SSBOND 9 CYS C 269 CYS C 319 1555 1555 2.04 CISPEP 1 SER A 22 PRO A 23 0 -2.26 CISPEP 2 ARG A 128 PRO A 129 0 3.51 CISPEP 3 GLY A 372 PRO A 373 0 -1.45 CISPEP 4 SER B 22 PRO B 23 0 -3.47 CISPEP 5 ARG B 128 PRO B 129 0 3.59 CISPEP 6 GLY B 372 PRO B 373 0 -0.78 CISPEP 7 SER C 22 PRO C 23 0 -2.83 CISPEP 8 ARG C 128 PRO C 129 0 3.47 CISPEP 9 GLY C 372 PRO C 373 0 -1.39 SITE 1 AC1 18 GLY A 11 GLN A 12 GLY A 13 LEU A 30 SITE 2 AC1 18 ASP A 32 GLY A 34 VAL A 69 PRO A 70 SITE 3 AC1 18 TYR A 71 THR A 72 GLN A 73 ILE A 126 SITE 4 AC1 18 ASP A 228 GLY A 230 THR A 231 THR A 232 SITE 5 AC1 18 ARG A 235 HOH A 395 SITE 1 AC2 18 GLY B 11 GLN B 12 GLY B 13 ASP B 32 SITE 2 AC2 18 GLY B 34 VAL B 69 PRO B 70 TYR B 71 SITE 3 AC2 18 THR B 72 GLN B 73 ILE B 126 ASP B 228 SITE 4 AC2 18 GLY B 230 THR B 231 THR B 232 ARG B 235 SITE 5 AC2 18 HOH B 394 HOH B 397 SITE 1 AC3 18 GLY C 11 GLN C 12 GLY C 13 LEU C 30 SITE 2 AC3 18 ASP C 32 GLY C 34 VAL C 69 PRO C 70 SITE 3 AC3 18 TYR C 71 THR C 72 GLN C 73 ILE C 126 SITE 4 AC3 18 ASP C 228 GLY C 230 THR C 231 THR C 232 SITE 5 AC3 18 ARG C 235 HOH C 394 CRYST1 82.547 101.299 102.218 90.00 104.16 90.00 P 1 21 1 6 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 0.012114 0.000000 0.003056 0.00000 SCALE2 0.000000 0.009872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010089 0.00000