HEADER HYDROLASE 10-JUL-12 4B1C TITLE NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL DESIGN TO AB- TITLE 2 LOWERING IN BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 56-445; COMPND 5 SYNONYM: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 6 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, COMPND 7 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, LEAD GENERATION, STRUCTURE-BASED DRUG DESIGN, INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR F.RAHM,J.BLID,T.GINMAN,S.KARLSTROM,J.KIHLSTROM,K.KOLMODIN, AUTHOR 2 J.LINDSTROM,S.VON BERG,F.VON KIESERITZKY,C.SLIVO,B.SWAHN,J.VIKLUND, AUTHOR 3 L.OLSSON,P.JOHANSSON,S.EKETJALL,J.FALTING,F.JEPPSSON,K.STROMBERG, AUTHOR 4 J.JANSON,Y.GRAVENFORS REVDAT 3 14-FEB-18 4B1C 1 AUTHOR JRNL REVDAT 2 21-NOV-12 4B1C 1 JRNL REVDAT 1 10-OCT-12 4B1C 0 JRNL AUTH Y.GRAVENFORS,J.VIKLUND,J.BLID,T.GINMAN,S.KARLSTROM, JRNL AUTH 2 J.KIHLSTROM,K.KOLMODIN,J.LINDSTROM,S.VON BERG, JRNL AUTH 3 F.VON KIESERITZKY,K.BOGAR,C.SLIVO,B.M.SWAHN,L.L.OLSSON, JRNL AUTH 4 P.JOHANSSON,S.EKETJALL,J.FALTING,F.JEPPSSON,K.STROMBERG, JRNL AUTH 5 J.JANSON,F.RAHM JRNL TITL NEW AMINOIMIDAZOLES AS BETA-SECRETASE (BACE-1) INHIBITORS JRNL TITL 2 SHOWING AMYLOID-BETA (A BETA ) LOWERING IN BRAIN. JRNL REF J. MED. CHEM. V. 55 9297 2012 JRNL REFN ISSN 1520-4804 JRNL PMID 23017051 JRNL DOI 10.1021/JM300991N REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 24701 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1304 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1566 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 1.69000 REMARK 3 B33 (A**2) : -2.33000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.460 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3062 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4161 ; 1.295 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 6.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;31.026 ;23.810 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 487 ;12.498 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.386 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2374 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1858 ; 3.701 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3004 ; 4.796 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1204 ; 4.215 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 5.664 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4B1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1290053287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27406 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 26.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 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 23.98000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.26150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.79800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.26150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.98000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.79800 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 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 OE2 GLU A 125 NH2 ARG A 195 1.88 REMARK 500 OH TYR A 14 OE2 GLU A 339 2.04 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 122 -168.28 -77.46 REMARK 500 TRP A 197 -88.81 -141.32 REMARK 500 ALA A 272 128.78 -39.49 REMARK 500 ASN A 293 17.56 54.13 REMARK 500 ASP A 311 115.55 -162.03 REMARK 500 ASP A 363 -169.51 -123.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2260 DISTANCE = 5.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1B1 A 1504 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 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 CATALYTICDOMAIN. REMARK 900 RELATED ID: 1TQF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-124,671 REMARK 900 RELATED ID: 1UJJ RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C-TERMINAL PEPTIDEFROM BACE REMARK 900 RELATED ID: 1UJK RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C- TERMINALPHOSPHOPEPTIDE REMARK 900 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 -PEPTIDIC REMARK 900 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 LONGINHIBITOR WITH REMARK 900 ADDITIONAL UPSTREAM RESIDUES. REMARK 900 RELATED ID: 1XS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CYCLOAMIDE-URETHANE-DERIVED NOVELINHIBITOR REMARK 900 BOUND TO HUMAN BRAIN MEMAPSIN 2 (BETA- SECRETASE). REMARK 900 RELATED ID: 1YM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AUR200 REMARK 900 RELATED ID: 1YM4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AMK640 REMARK 900 RELATED ID: 2B8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-000384950 REMARK 900 RELATED ID: 2B8V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA-SECRETASE COMPLEXED WITH L-L000430, REMARK 900 469 REMARK 900 RELATED ID: 2FDP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITH AN AMINO- REMARK 900 ETHYLENE INHIBITOR REMARK 900 RELATED ID: 2VA5 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 8C REMARK 900 RELATED ID: 2VA6 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 24 REMARK 900 RELATED ID: 2VA7 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 27 REMARK 900 RELATED ID: 2VIE RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-1-BENZYL- 2-HYDROXY-3-((1,1, REMARK 900 5-TRIMETHYLHEXYL)AMINO)PROPYL)-3 -(ETHYLAMINO)-5-(2-OXOPYRROLIDIN-1- REMARK 900 YL)BENZAMIDE REMARK 900 RELATED ID: 2VIJ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- DIOXIDOTETRAHYDRO-2H-1,2- REMARK 900 THIAZIN-2-YL)-5-(ETHYLAMINO )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)- REMARK 900 3-(1,2,3 ,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)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-(PENTYLSULFONYL) BENZAMIDE REMARK 900 RELATED ID: 2VIZ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-(2-OXO-1- PYRROLIDINYL)-5-(PROPYLOXY) REMARK 900 BENZAMIDE REMARK 900 RELATED ID: 2VJ6 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- OXO-1-PYRROLIDINYL) REMARK 900 BENZAMIDE REMARK 900 RELATED ID: 2VJ7 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(ETHYLAMINO)-N-((1S, 2R)-2-HYDROXY-1- REMARK 900 (PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)- REMARK 900 5-(2-OXO-1-PYRROLIDINYL) BENZAMIDE REMARK 900 RELATED ID: 2VJ9 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-( CYCLOHEXYLAMINO)-2- REMARK 900 HYDROXY-1-(PHENYLMETHYL)PROPYL)-3-( ETHYLAMINO)-5-(2-OXO-1- REMARK 900 PYRROLIDINYL)BENZAMIDE REMARK 900 RELATED ID: 2VKM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRL-8234 BOUND TO BACE (BETA- SECRETASE) REMARK 900 RELATED ID: 2VNM RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 3-(1,1- DIOXIDOTETRAHYDRO-2H-1,2- REMARK 900 THIAZIN-2-YL)-5-(ETHYLAMINO )-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)- REMARK 900 3-(((3-( 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)- 2-HYDROXY-1- REMARK 900 (PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)- REMARK 900 1-METHYL-3,4-DIHYDRO-1H -(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)- 2-HYDROXY-3-(((3- REMARK 900 (METHYLOXY)PHENYL)METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-4-(2-OXO-1- REMARK 900 PYRROLIDINYL)-1H- INDOLE-6-CARBOXAMIDE REMARK 900 RELATED ID: 2WF0 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 4-ETHYL-N-((1S,2R)- 2-HYDROXY-1- REMARK 900 (PHENYLMETHYL)-3-(((3-(TRIFLUOROMETHYL) PHENYL)METHYL)AMINO)PROPYL)- REMARK 900 8-(2-OXO-1-PYRROLIDINYL)- 6-QUINOLINECARBOXAMIDE REMARK 900 RELATED ID: 2WF1 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 7-ETHYL-N-((1S,2R)- 2-HYDROXY-3-(((3- REMARK 900 (METHYLOXY)PHENYL(METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-1-METHYL-3, REMARK 900 4-DIHYDRO-1H-(1,2, 5)THIADIAZEPINO(3,4,5-HI)INDOLE-9-CARBOXAMIDE 2, REMARK 900 2 -DIOXIDE REMARK 900 RELATED ID: 2WF2 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 8-ETHYL-N-((1S,2R)- 2-HYDROXY-3-(((3- REMARK 900 (METHYLOXY)PHENYL)METHYL)AMINO)-1-( PHENYLMETHYL)PROPYL)-1-METHYL-3, REMARK 900 4,7,8-TETRAHYDRO-1H ,6H-(1,2,5)THIADIAZEPINO(5,4,3-DE)QUINOXALINE- REMARK 900 10 -CARBOXAMIDE 2,2-DIOXIDE REMARK 900 RELATED ID: 2WF3 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 6-(ETHYLAMINO)-N-((1S, 2R)-2-HYDROXY-3- REMARK 900 (((3-(METHYLOXY)PHENYL)METHYL)AMINO)- 1-(PHENYLMETHYL)PROPYL)-1- REMARK 900 METHYL-1,3,4,5-TETRAHYDRO -2,1-BENZOTHIAZEPINE-8-CARBOXAMIDE 2,2- REMARK 900 DIOXIDE REMARK 900 RELATED ID: 2WF4 RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH 6-ETHYL-1-METHYL-N -((1S)-2-OXO-1- REMARK 900 (PHENYLMETHYL)-3-(TETRAHYDRO-2H-PYRAN -4-YLAMINO)PROPYL)-1,3,4,6- REMARK 900 TETRAHYDRO(1,2) 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 CYCLOHEXANECARBOXYLIC REMARK 900 ACID (2-(2-AM INO-6-PHENOXY-4H- QUINAZOLIN-3-YL)-2 -CYCLOHEXYL- REMARK 900 ETHYL)-AMIDE REMARK 900 RELATED ID: 2XFI RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-((METHYLSULFONYL)(PHENYL )AMINO)BENZAMIDE REMARK 900 RELATED ID: 2XFJ RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(2- OXO-1-PYRROLIDINYL) REMARK 900 BENZAMIDE REMARK 900 RELATED ID: 2XFK RELATED DB: PDB REMARK 900 HUMAN BACE-1 IN COMPLEX WITH N-((1S,2R)-3-(((1S)- 2- REMARK 900 (CYCLOHEXYLAMINO)-1-METHYL-2-OXOETHYL)AMINO)-2- HYDROXY-1- REMARK 900 (PHENYLMETHYL)PROPYL)-3-(ETHYLAMINO)-5-(( METHYLSULFONYL)(PHENYL) REMARK 900 AMINO)BENZAMIDE REMARK 900 RELATED ID: 4ACU RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL STRUCTURE OF REMARK 900 BETA SECRETASE COMPLEXED WITH COMPOUND 14 REMARK 900 RELATED ID: 4ACX RELATED DB: PDB REMARK 900 AMINOIMIDAZOLES AS BACE-1 INHIBITORS. X-RAY CRYSTAL STRUCTURE OF REMARK 900 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 BRAIN REMARK 900 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 BRAIN REMARK 900 REDUCTION OF BETA-AMYLOID PEPTIDES (COMPOUND (R )-41) REMARK 900 RELATED ID: 4B05 RELATED DB: PDB REMARK 900 PRECLINICAL CHARACTERIZATION OF AZD3839, A NOVEL CLINICAL CANDIDATE REMARK 900 BACE1 INHIBITOR FOR THE TREATMENT OF ALZHEIMER DISEASE REMARK 900 RELATED ID: 4B0Q RELATED DB: PDB REMARK 900 LEAD GENERATION OF BACE1 INHIBITORS BY COUPLING NON- AMIDINE NEW REMARK 900 WARHEADS TO A KNOWN BINDING SCAFFOLD REMARK 900 RELATED ID: 4B1D RELATED DB: PDB REMARK 900 NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL DESIGN TO REMARK 900 AB-LOWERING IN BRAIN REMARK 900 RELATED ID: 4B1E RELATED DB: PDB REMARK 900 NEW AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM RATIONAL DESIGN TO REMARK 900 AB-LOWERING IN BRAIN DBREF 4B1C A 497 502 UNP P56817 BACE1_HUMAN 56 61 DBREF 4B1C A 1 384 UNP P56817 BACE1_HUMAN 62 445 SEQADV 4B1C LYS A 497 UNP P56817 ARG 56 CONFLICT SEQADV 4B1C LYS A 498 UNP P56817 ARG 57 CONFLICT SEQRES 1 A 375 LYS LYS GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG SEQRES 2 A 375 GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL SEQRES 3 A 375 GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR SEQRES 4 A 375 GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO SEQRES 5 A 375 PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR SEQRES 6 A 375 TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR SEQRES 7 A 375 GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SEQRES 8 A 375 SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN SEQRES 9 A 375 ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN SEQRES 10 A 375 GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA SEQRES 11 A 375 GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE SEQRES 12 A 375 ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SEQRES 13 A 375 SER LEU GLN LEU CYS GLY GLY GLY SER MET ILE ILE GLY SEQRES 14 A 375 GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR SEQRES 15 A 375 THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE SEQRES 16 A 375 VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP SEQRES 17 A 375 CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER SEQRES 18 A 375 GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU SEQRES 19 A 375 ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER THR GLU SEQRES 20 A 375 LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL SEQRES 21 A 375 CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO SEQRES 22 A 375 VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SEQRES 23 A 375 SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG SEQRES 24 A 375 PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR SEQRES 25 A 375 LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET SEQRES 26 A 375 GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP SEQRES 27 A 375 ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS SEQRES 28 A 375 HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY SEQRES 29 A 375 PRO PHE VAL THR LEU GLU ASP CYS GLY TYR ASN HET DMS A1503 4 HET 1B1 A1504 25 HETNAM DMS DIMETHYL SULFOXIDE HETNAM 1B1 (2R)-2-CYCLOPROPYL-5-METHYL-2-[3-(5-PROP-1-YN-1- HETNAM 2 1B1 YLPYRIDIN-3-YL)PHENYL]-2H-IMIDAZOL-4-AMINE FORMUL 2 DMS C2 H6 O S FORMUL 3 1B1 C21 H20 N4 FORMUL 4 HOH *260(H2 O) HELIX 1 1 SER A 500 VAL A 3 1 6 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 SER A 182 5 3 HELIX 6 6 ASP A 216 TYR A 222 5 7 HELIX 7 7 LYS A 238 SER A 252 1 15 HELIX 8 8 PRO A 258 LEU A 263 1 6 HELIX 9 9 PRO A 276 PHE A 280 5 5 HELIX 10 10 LEU A 301 TYR A 305 1 5 HELIX 11 11 ASP A 311 SER A 315 5 5 HELIX 12 12 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 PRO A 70 0 SHEET 2 AB 2 LYS A 75 SER A 86 -1 O TRP A 76 N VAL A 69 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 VAL A 343 N LEU A 152 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 GLU A 200 VAL A 201 0 SHEET 2 AD 5 SER A 225 VAL A 227 -1 O SER A 225 N VAL A 201 SHEET 3 AD 5 THR A 331 MET A 333 1 O THR A 331 N ILE A 226 SHEET 4 AD 5 LEU A 234 PRO A 237 -1 O ARG A 235 N VAL A 332 SHEET 5 AD 5 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 AE 5 GLN A 211 ASP A 212 0 SHEET 2 AE 5 ILE A 203 ILE A 208 -1 O ILE A 208 N GLN A 211 SHEET 3 AE 5 ILE A 283 MET A 288 -1 O SER A 284 N GLU A 207 SHEET 4 AE 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 AE 5 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 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 2.04 CISPEP 1 SER A 22 PRO A 23 0 -6.30 CISPEP 2 ARG A 128 PRO A 129 0 6.83 CISPEP 3 TYR A 222 ASP A 223 0 4.53 CISPEP 4 GLY A 372 PRO A 373 0 0.11 SITE 1 AC1 4 GLY A 230 THR A 231 THR A 232 HOH A2175 SITE 1 AC2 14 SER A 10 GLN A 12 GLY A 13 ASP A 32 SITE 2 AC2 14 TYR A 71 PHE A 108 TRP A 115 ILE A 118 SITE 3 AC2 14 ASP A 228 SER A 229 GLY A 230 THR A 231 SITE 4 AC2 14 ALA A 335 HOH A2259 CRYST1 47.960 75.596 104.523 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 0.020851 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009567 0.00000