HEADER HYDROLASE 16-AUG-12 4B77 TITLE AMINOIMIDAZOLES AS BACE-1 INHIBITORS: FROM DE NOVO DESIGN TITLE 2 TO AB-LOWERING IN BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 58-445; 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, LEAD GENERATION, STRUCTURE-BASED 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 4B77 1 JRNL REVDAT 1 26-JUN-13 4B77 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 92.44 REMARK 3 NUMBER OF REFLECTIONS : 31605 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) : 0.19783 REMARK 3 R VALUE (WORKING SET) : 0.19526 REMARK 3 FREE R VALUE : 0.24828 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1668 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) : 1.800 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.847 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1845 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.310 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.397 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2987 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.474 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.81 REMARK 3 B22 (A**2) : 0.78 REMARK 3 B33 (A**2) : -1.60 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.154 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.417 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3133 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 6 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4273 ; 1.487 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12 ; 0.054 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 390 ; 6.914 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;34.474 ;23.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;13.881 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.692 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 463 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2428 ; 0.007 ; 0.021 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 1.20 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 4B77 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-53784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-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 : CCD 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 : 34894 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 24.51 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.7 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.30 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.7 REMARK 200 R MERGE FOR SHELL (I) : 0.51 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.00 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 23.94250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.30650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.81800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.30650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.94250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.81800 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 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 -88.13 -139.49 REMARK 500 ASN A 209 56.88 39.04 REMARK 500 LYS A 238 -55.90 -28.66 REMARK 500 ALA A 272 121.43 -37.36 REMARK 500 ALA A 323 37.56 -99.67 REMARK 500 CYS A 359 32.05 -98.45 REMARK 500 ASP A 363 -159.05 -116.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 54M A1504 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: 4B70 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: 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 4B77 A 499 502 UNP P56817 BACE1_HUMAN 58 61 DBREF 4B77 A 1 384 UNP P56817 BACE1_HUMAN 62 445 SEQRES 1 A 388 GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SEQRES 2 A 388 SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER SEQRES 3 A 388 PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SEQRES 4 A 388 SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU SEQRES 5 A 388 HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG SEQRES 6 A 388 ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY SEQRES 7 A 388 LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE SEQRES 8 A 388 PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA SEQRES 9 A 388 ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER SEQRES 10 A 388 ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE SEQRES 11 A 388 ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER SEQRES 12 A 388 LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU SEQRES 13 A 388 GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU SEQRES 14 A 388 VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY SEQRES 15 A 388 ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR SEQRES 16 A 388 PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL SEQRES 17 A 388 ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS SEQRES 18 A 388 LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY SEQRES 19 A 388 THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA SEQRES 20 A 388 ALA VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS SEQRES 21 A 388 PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS SEQRES 22 A 388 TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL SEQRES 23 A 388 ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER SEQRES 24 A 388 PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO SEQRES 25 A 388 VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS SEQRES 26 A 388 PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY SEQRES 27 A 388 ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG SEQRES 28 A 388 ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS SEQRES 29 A 388 VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO SEQRES 30 A 388 PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR HET DMS A1503 4 HET 54M A1504 26 HETNAM 54M (5R)-5-(4-METHOXYPHENYL)-5-(3-PYRIMIDIN-5- HETNAM 2 54M YLPHENYL)-3,4-DIHYDROPYRROL-2-AMINE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 54M C21 H20 N4 O FORMUL 3 DMS C2 H6 O S FORMUL 4 HOH *222(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 216 TYR A 222 5 7 HELIX 5 5 LYS A 238 SER A 252 1 15 HELIX 6 6 PRO A 258 LEU A 263 1 6 HELIX 7 7 PRO A 276 PHE A 280 5 5 HELIX 8 8 LEU A 301 TYR A 305 1 5 HELIX 9 9 ASP A 311 SER A 315 5 5 HELIX 10 10 GLY A 334 GLU A 339 1 6 SHEET 1 AA 3 ARG A 61 TYR A 71 0 SHEET 2 AA 3 GLY A 74 SER A 86 -1 O GLY A 74 N TYR A 71 SHEET 3 AA 3 TYR A 14 VAL A 20 -1 O THR A 19 N SER A 86 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 GLU A 200 VAL A 201 0 SHEET 2 AC 5 SER A 225 VAL A 227 -1 O SER A 225 N VAL A 201 SHEET 3 AC 5 THR A 331 MET A 333 1 O THR A 331 N ILE A 226 SHEET 4 AC 5 LEU A 234 PRO A 237 -1 O ARG A 235 N VAL A 332 SHEET 5 AC 5 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 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 3 VAL A 268 GLN A 271 0 SHEET 2 AE 3 ASP A 317 PHE A 322 -1 O ASP A 318 N TRP A 270 SHEET 3 AE 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 2.06 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.00 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.03 CISPEP 1 SER A 22 PRO A 23 0 -3.80 CISPEP 2 ARG A 128 PRO A 129 0 -0.42 CISPEP 3 TYR A 222 ASP A 223 0 2.53 CISPEP 4 GLY A 372 PRO A 373 0 2.43 SITE 1 AC1 1 GLY A 34 SITE 1 AC2 17 GLY A 11 GLN A 12 GLY A 13 LEU A 30 SITE 2 AC2 17 ASP A 32 GLY A 34 SER A 35 ASN A 37 SITE 3 AC2 17 VAL A 69 TYR A 71 TRP A 76 ILE A 110 SITE 4 AC2 17 ILE A 118 ASP A 228 GLY A 230 HOH A2009 SITE 5 AC2 17 HOH A2148 CRYST1 47.885 75.636 104.613 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 0.020883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009559 0.00000