HEADER HYDROLASE 16-AUG-12 4B70 TITLE AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM DE NOVO DESIGN TO TITLE 2 AB-LOWERING IN BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 61-445; COMPND 5 SYNONYM: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 6 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME COMPND 7 1, MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, HYDROLASE INHIBITOR, LEAD GENERATION, STRUCTURE-BASED KEYWDS 2 DRUG DESIGN EXPDTA X-RAY DIFFRACTION AUTHOR Y.GRAVENFORS,J.BLID,T.GINMAN,S.KARLSTROM,J.KIHLSTROM,K.KOLMODIN, AUTHOR 2 J.LINDSTROM,S.BERG,F.KIESERITZKY,C.SLIVO,B.SWAHN,J.VIKLUND,L.OLSSON, AUTHOR 3 P.JOHANSSON,S.EKETJALL,J.FALTING,F.JEPPSSON,K.STROMBERG,J.JANSON, AUTHOR 4 F.RAHM REVDAT 2 03-JUL-13 4B70 1 JRNL REVDAT 1 26-JUN-13 4B70 0 JRNL AUTH T.GINMAN,J.VIKLUND,J.MALMSTROM,J.BLID,R.EMOND,R.FORSBLOM, JRNL AUTH 2 A.JOHANSSON,A.KERS,F.LAKE,F.SEHGELMEBLE,K.J.STERKY,M.BERGH, JRNL AUTH 3 A.LINDGREN,P.JOHANSSON,F.JEPPSSON,J.FALTING,Y.GRAVENFORS, JRNL AUTH 4 F.RAHM JRNL TITL CORE REFINEMENT TOWARD PERMEABLE BETA-SECRETASE (BACE-1) JRNL TITL 2 INHIBITORS WITH LOW HERG ACTIVITY. JRNL REF J.MED.CHEM. V. 56 4181 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23126626 JRNL DOI 10.1021/JM3011349 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,WOMACK; REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.02 REMARK 3 NUMBER OF REFLECTIONS : 46412 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) : 0.2448 REMARK 3 R VALUE (WORKING SET) : 0.2430 REMARK 3 FREE R VALUE : 0.2806 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.08 REMARK 3 FREE R VALUE TEST SET COUNT : 2358 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.02 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3370 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.4427 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3186 REMARK 3 BIN R VALUE (WORKING SET) : 0.4430 REMARK 3 BIN FREE R VALUE : 0.4374 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.46 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 184 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 : 2947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.9091 REMARK 3 B22 (A**2) : -0.6235 REMARK 3 B33 (A**2) : 3.5326 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.285 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.133 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.127 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.127 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.124 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 : 0.9339 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.9066 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3059 ; 2.00 ; HARMONIC REMARK 3 BOND ANGLES : 4170 ; 2.00 ; HARMONIC REMARK 3 TORSION ANGLES : 1024 ; 2.00 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 72 ; 2.00 ; HARMONIC REMARK 3 GENERAL PLANES : 457 ; 5.00 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3059 ; 20.00 ; 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 : 392 ; 5.00 ; 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 : 3744 ; 4.00 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.13 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.88 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.79 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY REMARK 4 REMARK 4 4B70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-12. REMARK 100 THE PDBE ID CODE IS EBI-53777. 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 : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE (R-AXIS HTC) REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46458 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.60 REMARK 200 RESOLUTION RANGE LOW (A) : 30.56 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 3.7 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.70 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.8 REMARK 200 R MERGE FOR SHELL (I) : 0.55 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.31500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.45000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.45000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.31500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.61000 REMARK 290 SMTRY3 4 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 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 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 TRP A 197 -82.96 -141.37 REMARK 500 ALA A 323 35.75 -91.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 TYR A 305 24.5 L L OUTSIDE RANGE REMARK 500 SER A 315 24.8 L L OUTSIDE RANGE 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 WM9 A1503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FKN RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-SECRETASE COMPLEXED WITH INHIBITOR REMARK 900 RELATED ID: 1M4H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED REMARK 900 WITHINHIBITOR OM00-3 REMARK 900 RELATED ID: 1PY1 RELATED DB: PDB REMARK 900 COMPLEX OF GGA1-VHS DOMAIN AND BETA-SECRETASE C- REMARK 900 TERMINALPHOSPHOPEPTIDE REMARK 900 RELATED ID: 1SGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE REMARK 900 CATALYTICDOMAIN. REMARK 900 RELATED ID: 1TQF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH REMARK 900 L-124,671 REMARK 900 RELATED ID: 1UJJ RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C-TERMINAL REMARK 900 PEPTIDEFROM BACE REMARK 900 RELATED ID: 1UJK RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C- REMARK 900 TERMINALPHOSPHOPEPTIDE FROM BACE REMARK 900 RELATED ID: 1W50 RELATED DB: PDB REMARK 900 APO STRUCTURE OF BACE (BETA SECRETASE) REMARK 900 RELATED ID: 1W51 RELATED DB: PDB REMARK 900 BACE (BETA SECRETASE) IN COMPLEX WITH A NANOMOLAR NON REMARK 900 -PEPTIDIC INHIBITOR REMARK 900 RELATED ID: 1XN2 RELATED DB: PDB REMARK 900 NEW SUBSTRATE BINDING POCKETS FOR BETA-SECRETASE. REMARK 900 RELATED ID: 1XN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE BOUND TO A REMARK 900 LONGINHIBITOR WITH ADDITIONAL UPSTREAM RESIDUES. REMARK 900 RELATED ID: 1XS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CYCLOAMIDE-URETHANE-DERIVED REMARK 900 NOVELINHIBITOR BOUND TO HUMAN BRAIN MEMAPSIN 2 (BETA- REMARK 900 SECRETASE). REMARK 900 RELATED ID: 1YM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED REMARK 900 WITHNVP-AUR200 REMARK 900 RELATED ID: 1YM4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED REMARK 900 WITHNVP-AMK640 REMARK 900 RELATED ID: 2B8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH REMARK 900 L-000384950 REMARK 900 RELATED ID: 2B8V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA-SECRETASE COMPLEXED WITH REMARK 900 L-L000430,469 REMARK 900 RELATED ID: 2FDP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITH AN REMARK 900 AMINO-ETHYLENE INHIBITOR REMARK 900 RELATED ID: 2VA5 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED REMARK 900 WITH COMPOUND 8C REMARK 900 RELATED ID: 2VA6 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED REMARK 900 WITH COMPOUND 24 REMARK 900 RELATED ID: 2VA7 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED REMARK 900 WITH COMPOUND 27 REMARK 900 RELATED ID: 2VIE RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-1-BENZYL- REMARK 900 2-HYDROXY-3-((1,1,5-TRIMETHYLHEXYL)AMINO)PROPYL)-3 REMARK 900 -(ETHYLAMINO)-5-(2-OXOPYRROLIDIN-1-YL)BENZAMIDE REMARK 900 RELATED ID: 2VIJ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- REMARK 900 DIOXIDOTETRAHYDRO-2H-1,2-THIAZIN-2-YL)-5-(ETHYLAMINO REMARK 900 )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(1,2,3 REMARK 900 ,4-TETRAHYDRO-1-NAPHTHALENYLAMINO)PROPYL)BENZAMIDE REMARK 900 RELATED ID: 2VIY RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(PENTYLSULFONYL) REMARK 900 BENZAMIDE REMARK 900 RELATED ID: 2VIZ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(2-OXO-1- REMARK 900 PYRROLIDINYL)-5-(PROPYLOXY)BENZAMIDE REMARK 900 RELATED ID: 2VJ6 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- REMARK 900 OXO-1-PYRROLIDINYL)BENZAMIDE REMARK 900 RELATED ID: 2VJ7 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(ETHYLAMINO)-N-((1S, REMARK 900 2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) REMARK 900 PHENYL)METHYL)AMINO)PROPYL)-5-(2-OXO-1-PYRROLIDINYL) REMARK 900 BENZAMIDE REMARK 900 RELATED ID: 2VJ9 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-( REMARK 900 CYCLOHEXYLAMINO)-2-HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-( REMARK 900 ETHYLAMINO)-5-(2-OXO-1-PYRROLIDINYL)BENZAMIDE REMARK 900 RELATED ID: 2VKM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRL-8234 BOUND TO BACE (BETA- REMARK 900 SECRETASE) REMARK 900 RELATED ID: 2VNM RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- REMARK 900 DIOXIDOTETRAHYDRO-2H-1,2-THIAZIN-2-YL)-5-(ETHYLAMINO REMARK 900 )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-( REMARK 900 TRIFLUOROMETHYL)PHENYL)METHYL)AMINO)PROPYL)BENZAMIDE REMARK 900 RELATED ID: 2VNN RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 7-ETHYL-N-((1S,2R)- REMARK 900 2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) REMARK 900 PHENYL)METHYL)AMINO)PROPYL)-1-METHYL-3,4-DIHYDRO-1H REMARK 900 -(1,2,5)THIADIAZEPINO(3,4,5-HI)INDOLE-9- REMARK 900 CARBOXAMIDE 2,2-DIOXIDE REMARK 900 RELATED ID: 2WEZ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 1-ETHYL-N-((1S,2R)- REMARK 900 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)-1-( REMARK 900 PHENYLMETHYL)PROPYL)-4-(2-OXO-1-PYRROLIDINYL)-1H- REMARK 900 INDOLE-6-CARBOXAMIDE REMARK 900 RELATED ID: 2WF0 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 4-ETHYL-N-((1S,2R)- REMARK 900 2-HYDROXY-1-(PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) REMARK 900 PHENYL)METHYL)AMINO)PROPYL)-8-(2-OXO-1-PYRROLIDINYL)- REMARK 900 6-QUINOLINECARBOXAMIDE REMARK 900 RELATED ID: 2WF1 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 7-ETHYL-N-((1S,2R)- REMARK 900 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL(METHYL)AMINO)-1-( REMARK 900 PHENYLMETHYL)PROPYL)-1-METHYL-3,4-DIHYDRO-1H-(1,2, REMARK 900 5)THIADIAZEPINO(3,4,5-HI)INDOLE-9-CARBOXAMIDE 2,2 REMARK 900 -DIOXIDE REMARK 900 RELATED ID: 2WF2 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 8-ETHYL-N-((1S,2R)- REMARK 900 2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)-1-( REMARK 900 PHENYLMETHYL)PROPYL)-1-METHYL-3,4,7,8-TETRAHYDRO-1H REMARK 900 ,6H-(1,2,5)THIADIAZEPINO(5,4,3-DE)QUINOXALINE-10 REMARK 900 -CARBOXAMIDE 2,2-DIOXIDE REMARK 900 RELATED ID: 2WF3 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 6-(ETHYLAMINO)-N-((1S, REMARK 900 2R)-2-HYDROXY-3-(((3-(METHYLOXY)PHENYL)METHYL)AMINO)- REMARK 900 1-(PHENYLMETHYL)PROPYL)-1-METHYL-1,3,4,5-TETRAHYDRO REMARK 900 -2,1-BENZOTHIAZEPINE-8-CARBOXAMIDE 2,2-DIOXIDE REMARK 900 RELATED ID: 2WF4 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 6-ETHYL-1-METHYL-N REMARK 900 -((1S)-2-OXO-1-(PHENYLMETHYL)-3-(TETRAHYDRO-2H-PYRAN REMARK 900 -4-YLAMINO)PROPYL)-1,3,4,6-TETRAHYDRO(1,2) REMARK 900 THIAZEPINO(5,4,3-CD)INDOLE-8-CARBOXAMIDE 2,2- REMARK 900 DIOXIDE REMARK 900 RELATED ID: 2WJO RELATED DB: PDB REMARK 900 HUMAN BACE (BETA SECRETASE) IN COMPLEX WITH REMARK 900 CYCLOHEXANECARBOXYLIC ACID (2-(2-AM INO-6-PHENOXY-4H- REMARK 900 QUINAZOLIN-3-YL)-2 -CYCLOHEXYL-ETHYL)-AMIDE REMARK 900 RELATED ID: 2XFI RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-((METHYLSULFONYL)(PHENYL REMARK 900 )AMINO)BENZAMIDE REMARK 900 RELATED ID: 2XFJ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- REMARK 900 OXO-1-PYRROLIDINYL)BENZAMIDE REMARK 900 RELATED ID: 2XFK RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- REMARK 900 2-(CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(( REMARK 900 METHYLSULFONYL)(PHENYL)AMINO)BENZAMIDE REMARK 900 RELATED ID: 4ACU RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL REMARK 900 STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 14 REMARK 900 RELATED ID: 4ACX RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL REMARK 900 STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 23 REMARK 900 RELATED ID: 4AZY RELATED DB: PDB REMARK 900 DESIGN AND SYNTHESIS OF BACE1 INHIBITORS WITH IN VIVO REMARK 900 BRAIN REDUCTION OF BETA-AMYLOID PEPTIDES (COMPOUND 10) REMARK 900 RELATED ID: 4B00 RELATED DB: PDB REMARK 900 DESIGN AND SYNTHESIS OF BACE1 INHIBITORS WITH IN VIVO REMARK 900 BRAIN REDUCTION OF BETA-AMYLOID PEPTIDES (COMPOUND (R REMARK 900 )-41) REMARK 900 RELATED ID: 4B05 RELATED DB: PDB REMARK 900 PRECLINICAL CHARACTERIZATION OF AZD3839, A NOVEL CLINICAL REMARK 900 CANDIDATE BACE1 INHIBITOR FOR THE TREATMENT OF REMARK 900 ALZHEIMER DISEASE REMARK 900 RELATED ID: 4B0Q RELATED DB: PDB REMARK 900 LEAD GENERATION OF BACE1 INHIBITORS BY COUPLING NON- REMARK 900 AMIDINE NEW WARHEADS TO A KNOWN BINDING SCAFFOLD REMARK 900 RELATED ID: 4B1C RELATED DB: PDB REMARK 900 NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL REMARK 900 DESIGN TO AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B1D RELATED DB: PDB REMARK 900 NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL REMARK 900 DESIGN TO AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B1E RELATED DB: PDB REMARK 900 NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL REMARK 900 DESIGN TO AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B72 RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM DE NOVO REMARK 900 DESIGN TO AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B77 RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM DE NOVO REMARK 900 DESIGN TO AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B78 RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM DE NOVO REMARK 900 DESIGN TO AB-LOWERING IN BRAIN DBREF 4B70 A 502 502 UNP P56817 BACE1_HUMAN 61 61 DBREF 4B70 A 1 384 UNP P56817 BACE1_HUMAN 62 445 SEQRES 1 A 385 VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER GLY GLN SEQRES 2 A 385 GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO PRO GLN SEQRES 3 A 385 THR LEU ASN ILE LEU VAL ASP THR GLY SER SER ASN PHE SEQRES 4 A 385 ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS ARG TYR SEQRES 5 A 385 TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP LEU ARG SEQRES 6 A 385 LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS TRP GLU SEQRES 7 A 385 GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO HIS GLY SEQRES 8 A 385 PRO ASN VAL THR VAL ARG ALA ASN ILE ALA ALA ILE THR SEQRES 9 A 385 GLU SER ASP LYS PHE PHE ILE ASN GLY SER ASN TRP GLU SEQRES 10 A 385 GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA ARG PRO SEQRES 11 A 385 ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU VAL LYS SEQRES 12 A 385 GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN LEU CYS SEQRES 13 A 385 GLY ALA GLY PHE PRO LEU ASN GLN SER GLU VAL LEU ALA SEQRES 14 A 385 SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE ASP HIS SEQRES 15 A 385 SER LEU TYR THR GLY SER LEU TRP TYR THR PRO ILE ARG SEQRES 16 A 385 ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG VAL GLU SEQRES 17 A 385 ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS GLU TYR SEQRES 18 A 385 ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR THR ASN SEQRES 19 A 385 LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA VAL LYS SEQRES 20 A 385 SER ILE LYS ALA ALA SER SER THR GLU LYS PHE PRO ASP SEQRES 21 A 385 GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP GLN ALA SEQRES 22 A 385 GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SER LEU SEQRES 23 A 385 TYR LEU MET GLY GLU VAL THR ASN GLN SER PHE ARG ILE SEQRES 24 A 385 THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL GLU ASP SEQRES 25 A 385 VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE ALA ILE SEQRES 26 A 385 SER GLN SER SER THR GLY THR VAL MET GLY ALA VAL ILE SEQRES 27 A 385 MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA ARG LYS SEQRES 28 A 385 ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL HIS ASP SEQRES 29 A 385 GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE VAL THR SEQRES 30 A 385 LEU ASP MET GLU ASP CYS GLY TYR HET WM9 A1503 21 HETNAM WM9 (2S)-2-[3-(3-CHLOROPHENYL)PHENYL]-2-METHYL-5, HETNAM 2 WM9 6-DIHYDRO-1,3-OXAZIN-4-AMINE FORMUL 2 WM9 C17 H17 CL N2 O FORMUL 3 HOH *325(H2 O) HELIX 1 1 GLN A 53 SER A 57 5 5 HELIX 2 2 TYR A 123 ALA A 127 5 5 HELIX 3 3 PRO A 135 THR A 144 1 10 HELIX 4 4 ASP A 180 SER A 182 5 3 HELIX 5 5 ASP A 216 TYR A 222 5 7 HELIX 6 6 LYS A 238 SER A 252 1 15 HELIX 7 7 PRO A 258 LEU A 263 1 6 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 ASP A 311 SER A 315 5 5 HELIX 11 11 GLY A 334 GLU A 339 1 6 SHEET 1 AA 2 LEU A 6 LYS A 9 0 SHEET 2 AA 2 GLY A 13 VAL A 20 -1 O GLY A 13 N LYS A 9 SHEET 1 AB 2 ARG A 61 TYR A 71 0 SHEET 2 AB 2 GLY A 74 SER A 86 -1 O GLY A 74 N TYR A 71 SHEET 1 AC 5 GLY A 172 ILE A 176 0 SHEET 2 AC 5 PHE A 150 LEU A 154 -1 O SER A 151 N ILE A 175 SHEET 3 AC 5 PHE A 341 ASP A 346 -1 O PHE A 341 N LEU A 154 SHEET 4 AC 5 ARG A 351 SER A 357 -1 O ARG A 351 N ASP A 346 SHEET 5 AC 5 TYR A 184 PRO A 192 -1 O THR A 185 N VAL A 356 SHEET 1 AD 5 GLN A 211 ASP A 212 0 SHEET 2 AD 5 ILE A 203 ILE A 208 -1 O ILE A 208 N GLN A 211 SHEET 3 AD 5 ILE A 283 MET A 288 -1 O SER A 284 N GLU A 207 SHEET 4 AD 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 AD 5 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 SHEET 1 AE 4 SER A 225 VAL A 227 0 SHEET 2 AE 4 THR A 331 MET A 333 1 O THR A 331 N ILE A 226 SHEET 3 AE 4 LEU A 234 PRO A 237 -1 O ARG A 235 N VAL A 332 SHEET 4 AE 4 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 AF 3 VAL A 268 GLN A 271 0 SHEET 2 AF 3 ASP A 317 PHE A 322 -1 O ASP A 318 N TRP A 270 SHEET 3 AF 3 LEU A 306 PRO A 308 -1 O ARG A 307 N LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.05 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.03 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.06 CISPEP 1 SER A 22 PRO A 23 0 -5.13 CISPEP 2 ARG A 128 PRO A 129 0 3.53 CISPEP 3 TYR A 222 ASP A 223 0 -1.64 CISPEP 4 GLY A 372 PRO A 373 0 -2.68 SITE 1 AC1 12 GLY A 11 GLN A 12 GLY A 13 ASP A 32 SITE 2 AC1 12 TYR A 71 PHE A 108 ILE A 110 ILE A 118 SITE 3 AC1 12 ASP A 228 SER A 229 GLY A 230 THR A 232 CRYST1 48.630 75.220 104.900 90.00 90.00 90.00 P 21 21 21 4 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 0.020563 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009533 0.00000