HEADER HYDROLASE/HYDROLASE INHIBITOR 26-JUN-12 4FRS TITLE STRUCTURE OF BACE IN COMPLEX WITH (S)-4-(3-CHLORO-5-(5-(PROP-1-YN-1- TITLE 2 YL)PYRIDIN-3-YL)THIOPHEN-2-YL)-1,4-DIMETHYL-6-OXOTETRAHYDROPYRIMIDIN- TITLE 3 2(1H)-IMINIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 5 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, COMPND 6 MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 7 EC: 3.4.23.46; COMPND 8 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: BACE1, BACE, KIAA1149; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ALZHEIMER'S, ASPARTYL PROTEASE, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.ORTH REVDAT 3 19-JUN-13 4FRS 1 JRNL REVDAT 2 21-NOV-12 4FRS 1 HETATM REVDAT 1 08-AUG-12 4FRS 0 JRNL AUTH A.W.STAMFORD,J.D.SCOTT,S.W.LI,S.BABU,D.TADESSE,R.HUNTER, JRNL AUTH 2 Y.WU,J.MISIASZEK,J.N.CUMMING,E.J.GILBERT,C.HUANG, JRNL AUTH 3 B.A.MCKITTRICK,L.HONG,T.GUO,Z.ZHU,C.STRICKLAND,P.ORTH, JRNL AUTH 4 J.H.VOIGT,M.E.KENNEDY,X.CHEN,R.KUVELKAR,R.HODGSON,L.A.HYDE, JRNL AUTH 5 K.COX,L.FAVREAU,E.M.PARKER,W.J.GREENLEE JRNL TITL DISCOVERY OF AN ORALLY AVAILABLE, BRAIN PENETRANT BACE1 JRNL TITL 2 INHIBITOR THAT AFFORDS ROBUST CNS A(BETA) REDUCTION JRNL REF ACS MED CHEM LETT V. 3 897 2012 JRNL REFN ISSN 1948-5875 JRNL PMID 23412139 JRNL DOI 10.1021/ML3001165 REMARK 2 REMARK 2 RESOLUTION. 1.70 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, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 106567 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4268 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 7850 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2463 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7533 REMARK 3 BIN R VALUE (WORKING SET) : 0.2438 REMARK 3 BIN FREE R VALUE : 0.3035 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.04 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 317 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 : 6050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 823 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.12220 REMARK 3 B22 (A**2) : -5.47460 REMARK 3 B33 (A**2) : 3.35240 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6302 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8588 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2092 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 160 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 935 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6302 ; 20.000 ; 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 : 802 ; 5.000 ; 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 : 7915 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.09 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.68 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4FRS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-12. REMARK 100 THE RCSB ID CODE IS RCSB073274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 95 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 : RIGAKU FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119246 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 43.23650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.71350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.74750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.71350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.23650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.74750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 GLU A 53 REMARK 465 PRO A 54 REMARK 465 GLY A 55 REMARK 465 ARG A 56 REMARK 465 ARG A 57 REMARK 465 VAL A 373 REMARK 465 ALA A 374 REMARK 465 THR A 375 REMARK 465 ILE A 447 REMARK 465 GLU B 53 REMARK 465 PRO B 54 REMARK 465 GLY B 55 REMARK 465 ARG B 56 REMARK 465 VAL B 373 REMARK 465 ALA B 374 REMARK 465 THR B 375 REMARK 465 ILE B 447 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS A 203 NZ REMARK 470 GLN A 224 CG CD OE1 NE2 REMARK 470 GLU A 441 CG CD OE1 OE2 REMARK 470 GLN B 134 CD OE1 NE2 REMARK 470 ARG B 189 CZ NH1 NH2 REMARK 470 LYS B 203 NZ REMARK 470 GLN B 224 CG CD OE1 NE2 REMARK 470 GLU B 441 CG CD OE1 OE2 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 GLN A 134 -138.89 -71.85 REMARK 500 HIS A 150 57.19 -104.72 REMARK 500 PHE A 169 -62.04 -91.16 REMARK 500 ALA A 183 -169.70 -77.07 REMARK 500 TRP A 258 -82.47 -143.73 REMARK 500 ALA A 333 121.77 -38.85 REMARK 500 HIS B 150 55.41 -107.34 REMARK 500 TRP B 258 -80.25 -145.18 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 366 24.6 L L OUTSIDE RANGE REMARK 500 VAL A 397 24.6 L L OUTSIDE RANGE REMARK 500 ASN B 175 24.7 L L OUTSIDE RANGE REMARK 500 TYR B 366 24.6 L L OUTSIDE RANGE 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 A1027 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH B 715 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH B 865 DISTANCE = 7.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0V6 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0V6 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DJU RELATED DB: PDB REMARK 900 STRUCTURE OF BACE BOUND TO 2-IMINO-3-METHYL-5,5- REMARK 900 DIPHENYLIMIDAZOLIDIN-4-ONE REMARK 900 RELATED ID: 4DJV RELATED DB: PDB REMARK 900 STRUCTURE OF BACE BOUND TO 2-IMINO-5-(3'-METHOXY-[1,1'- REMARK 900 BIPHENYL]-3-YL)-3-METHYL-5-PHENYLIMIDAZOLIDIN-4-ONE REMARK 900 RELATED ID: 4DJW RELATED DB: PDB REMARK 900 STRUCTURE OF BACE BOUND TO 2-IMINO-3-METHYL-5-PHENYL-5-(3- REMARK 900 (PYRIDIN-3-YL)PHENYL)IMIDAZOLIDIN-4-ONE REMARK 900 RELATED ID: 4DJX RELATED DB: PDB REMARK 900 STRUCTURE OF BACE BOUND TO 5-(3-(5-CHLOROPYRIDIN-3-YL) REMARK 900 PHENYL)-5-CYCLOPROPYL-2-IMINO-3-METHYLIMIDAZOLIDIN-4-ONE REMARK 900 RELATED ID: 4DJY RELATED DB: PDB REMARK 900 STRUCTURE OF BACE BOUND TO (R)-5-CYCLOPROPYL-2-IMINO-3- REMARK 900 METHYL-5-(3-(5-(PROP-1-YN-1-YL)PYRIDIN-3-YL)PHENYL) REMARK 900 IMIDAZOLIDIN-4-ONE DBREF 4FRS A 53 447 UNP P56817 BACE1_HUMAN 53 447 DBREF 4FRS B 53 447 UNP P56817 BACE1_HUMAN 53 447 SEQRES 1 A 395 GLU PRO GLY ARG ARG GLY SER PHE VAL GLU MET VAL ASP SEQRES 2 A 395 ASN LEU ARG GLY LYS SER GLY GLN GLY TYR TYR VAL GLU SEQRES 3 A 395 MET THR VAL GLY SER PRO PRO GLN THR LEU ASN ILE LEU SEQRES 4 A 395 VAL ASP THR GLY SER SER ASN PHE ALA VAL GLY ALA ALA SEQRES 5 A 395 PRO HIS PRO PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SEQRES 6 A 395 SER SER THR TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL SEQRES 7 A 395 PRO TYR THR GLN GLY LYS TRP GLU GLY GLU LEU GLY THR SEQRES 8 A 395 ASP LEU VAL SER ILE PRO HIS GLY PRO ASN VAL THR VAL SEQRES 9 A 395 ARG ALA ASN ILE ALA ALA ILE THR GLU SER ASP LYS PHE SEQRES 10 A 395 PHE ILE ASN GLY SER ASN TRP GLU GLY ILE LEU GLY LEU SEQRES 11 A 395 ALA TYR ALA GLU ILE ALA ARG PRO ASP ASP SER LEU GLU SEQRES 12 A 395 PRO PHE PHE ASP SER LEU VAL LYS GLN THR HIS VAL PRO SEQRES 13 A 395 ASN LEU PHE SER LEU GLN LEU CYS GLY ALA GLY PHE PRO SEQRES 14 A 395 LEU ASN GLN SER GLU VAL LEU ALA SER VAL GLY GLY SER SEQRES 15 A 395 MET ILE ILE GLY GLY ILE ASP HIS SER LEU TYR THR GLY SEQRES 16 A 395 SER LEU TRP TYR THR PRO ILE ARG ARG GLU TRP TYR TYR SEQRES 17 A 395 GLU VAL ILE ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP SEQRES 18 A 395 LEU LYS MET ASP CYS LYS GLU TYR ASN TYR ASP LYS SER SEQRES 19 A 395 ILE VAL ASP SER GLY THR THR ASN LEU ARG LEU PRO LYS SEQRES 20 A 395 LYS VAL PHE GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SEQRES 21 A 395 SER SER THR GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY SEQRES 22 A 395 GLU GLN LEU VAL CYS TRP GLN ALA GLY THR THR PRO TRP SEQRES 23 A 395 ASN ILE PHE PRO VAL ILE SER LEU TYR LEU MET GLY GLU SEQRES 24 A 395 VAL THR ASN GLN SER PHE ARG ILE THR ILE LEU PRO GLN SEQRES 25 A 395 GLN TYR LEU ARG PRO VAL GLU ASP VAL ALA THR SER GLN SEQRES 26 A 395 ASP ASP CYS TYR LYS PHE ALA ILE SER GLN SER SER THR SEQRES 27 A 395 GLY THR VAL MET GLY ALA VAL ILE MET GLU GLY PHE TYR SEQRES 28 A 395 VAL VAL PHE ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA SEQRES 29 A 395 VAL SER ALA CYS HIS VAL HIS ASP GLU PHE ARG THR ALA SEQRES 30 A 395 ALA VAL GLU GLY PRO PHE VAL THR LEU ASP MET GLU ASP SEQRES 31 A 395 CYS GLY TYR ASN ILE SEQRES 1 B 395 GLU PRO GLY ARG ARG GLY SER PHE VAL GLU MET VAL ASP SEQRES 2 B 395 ASN LEU ARG GLY LYS SER GLY GLN GLY TYR TYR VAL GLU SEQRES 3 B 395 MET THR VAL GLY SER PRO PRO GLN THR LEU ASN ILE LEU SEQRES 4 B 395 VAL ASP THR GLY SER SER ASN PHE ALA VAL GLY ALA ALA SEQRES 5 B 395 PRO HIS PRO PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SEQRES 6 B 395 SER SER THR TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL SEQRES 7 B 395 PRO TYR THR GLN GLY LYS TRP GLU GLY GLU LEU GLY THR SEQRES 8 B 395 ASP LEU VAL SER ILE PRO HIS GLY PRO ASN VAL THR VAL SEQRES 9 B 395 ARG ALA ASN ILE ALA ALA ILE THR GLU SER ASP LYS PHE SEQRES 10 B 395 PHE ILE ASN GLY SER ASN TRP GLU GLY ILE LEU GLY LEU SEQRES 11 B 395 ALA TYR ALA GLU ILE ALA ARG PRO ASP ASP SER LEU GLU SEQRES 12 B 395 PRO PHE PHE ASP SER LEU VAL LYS GLN THR HIS VAL PRO SEQRES 13 B 395 ASN LEU PHE SER LEU GLN LEU CYS GLY ALA GLY PHE PRO SEQRES 14 B 395 LEU ASN GLN SER GLU VAL LEU ALA SER VAL GLY GLY SER SEQRES 15 B 395 MET ILE ILE GLY GLY ILE ASP HIS SER LEU TYR THR GLY SEQRES 16 B 395 SER LEU TRP TYR THR PRO ILE ARG ARG GLU TRP TYR TYR SEQRES 17 B 395 GLU VAL ILE ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP SEQRES 18 B 395 LEU LYS MET ASP CYS LYS GLU TYR ASN TYR ASP LYS SER SEQRES 19 B 395 ILE VAL ASP SER GLY THR THR ASN LEU ARG LEU PRO LYS SEQRES 20 B 395 LYS VAL PHE GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SEQRES 21 B 395 SER SER THR GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY SEQRES 22 B 395 GLU GLN LEU VAL CYS TRP GLN ALA GLY THR THR PRO TRP SEQRES 23 B 395 ASN ILE PHE PRO VAL ILE SER LEU TYR LEU MET GLY GLU SEQRES 24 B 395 VAL THR ASN GLN SER PHE ARG ILE THR ILE LEU PRO GLN SEQRES 25 B 395 GLN TYR LEU ARG PRO VAL GLU ASP VAL ALA THR SER GLN SEQRES 26 B 395 ASP ASP CYS TYR LYS PHE ALA ILE SER GLN SER SER THR SEQRES 27 B 395 GLY THR VAL MET GLY ALA VAL ILE MET GLU GLY PHE TYR SEQRES 28 B 395 VAL VAL PHE ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA SEQRES 29 B 395 VAL SER ALA CYS HIS VAL HIS ASP GLU PHE ARG THR ALA SEQRES 30 B 395 ALA VAL GLU GLY PRO PHE VAL THR LEU ASP MET GLU ASP SEQRES 31 B 395 CYS GLY TYR ASN ILE HET 0V6 A 501 25 HET 0V6 B 501 25 HETNAM 0V6 (2Z,6S)-6-{3-CHLORO-5-[5-(PROP-1-YN-1-YL)PYRIDIN-3- HETNAM 2 0V6 YL]THIOPHEN-2-YL}-2-IMINO-3,6- HETNAM 3 0V6 DIMETHYLTETRAHYDROPYRIMIDIN-4(1H)-ONE FORMUL 3 0V6 2(C18 H17 CL N4 O S) FORMUL 5 HOH *823(H2 O) HELIX 1 1 GLN A 114 SER A 118 5 5 HELIX 2 2 TYR A 184 ALA A 188 5 5 HELIX 3 3 PRO A 196 THR A 205 1 10 HELIX 4 4 ASN A 223 SER A 230 1 8 HELIX 5 5 ASP A 241 SER A 243 5 3 HELIX 6 6 ASP A 277 TYR A 283 5 7 HELIX 7 7 LYS A 299 SER A 313 1 15 HELIX 8 8 PRO A 319 LEU A 324 1 6 HELIX 9 9 PRO A 337 PHE A 341 5 5 HELIX 10 10 LEU A 362 TYR A 366 1 5 HELIX 11 11 GLY A 395 GLU A 400 1 6 HELIX 12 12 ASP A 439 GLY A 444 5 6 HELIX 13 13 GLN B 114 SER B 118 5 5 HELIX 14 14 TYR B 184 ALA B 188 5 5 HELIX 15 15 PRO B 196 THR B 205 1 10 HELIX 16 16 ASN B 223 SER B 230 1 8 HELIX 17 17 ASP B 241 SER B 243 5 3 HELIX 18 18 ASP B 277 TYR B 283 5 7 HELIX 19 19 LYS B 299 SER B 313 1 15 HELIX 20 20 PRO B 319 LEU B 324 1 6 HELIX 21 21 PRO B 337 PHE B 341 5 5 HELIX 22 22 LEU B 362 TYR B 366 1 5 HELIX 23 23 GLY B 395 GLU B 400 1 6 HELIX 24 24 ASP B 439 GLY B 444 5 6 SHEET 1 A 8 LEU A 67 LYS A 70 0 SHEET 2 A 8 GLY A 74 VAL A 81 -1 O TYR A 76 N ARG A 68 SHEET 3 A 8 GLN A 86 ASP A 93 -1 O LEU A 88 N MET A 79 SHEET 4 A 8 GLY A 178 GLY A 181 1 O LEU A 180 N LEU A 91 SHEET 5 A 8 PHE A 99 GLY A 102 -1 N ALA A 100 O ILE A 179 SHEET 6 A 8 THR A 155 ASP A 167 1 O ILE A 163 N VAL A 101 SHEET 7 A 8 LYS A 136 SER A 147 -1 N GLU A 140 O ALA A 162 SHEET 8 A 8 ARG A 122 VAL A 130 -1 N LYS A 126 O LEU A 141 SHEET 1 B 4 LEU A 67 LYS A 70 0 SHEET 2 B 4 GLY A 74 VAL A 81 -1 O TYR A 76 N ARG A 68 SHEET 3 B 4 LYS A 136 SER A 147 -1 O SER A 147 N THR A 80 SHEET 4 B 4 ARG A 122 VAL A 130 -1 N LYS A 126 O LEU A 141 SHEET 1 C 5 GLY A 233 ILE A 237 0 SHEET 2 C 5 PHE A 211 LEU A 215 -1 N GLN A 214 O SER A 234 SHEET 3 C 5 PHE A 402 ASP A 407 -1 O PHE A 406 N PHE A 211 SHEET 4 C 5 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403 SHEET 5 C 5 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413 SHEET 1 D 5 GLU A 261 VAL A 262 0 SHEET 2 D 5 SER A 286 VAL A 288 -1 O SER A 286 N VAL A 262 SHEET 3 D 5 THR A 392 MET A 394 1 O MET A 394 N ILE A 287 SHEET 4 D 5 LEU A 295 PRO A 298 -1 N ARG A 296 O VAL A 393 SHEET 5 D 5 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297 SHEET 1 E 5 GLN A 272 ASP A 273 0 SHEET 2 E 5 ILE A 264 ILE A 269 -1 N ILE A 269 O GLN A 272 SHEET 3 E 5 ILE A 344 MET A 349 -1 O TYR A 347 N ARG A 266 SHEET 4 E 5 GLN A 355 ILE A 361 -1 O ILE A 361 N ILE A 344 SHEET 5 E 5 ALA A 430 VAL A 436 -1 O GLU A 432 N ARG A 358 SHEET 1 F 3 VAL A 329 TRP A 331 0 SHEET 2 F 3 ASP A 379 PHE A 383 -1 O ASP A 379 N TRP A 331 SHEET 3 F 3 LEU A 367 VAL A 370 -1 N ARG A 368 O LYS A 382 SHEET 1 G 8 LEU B 67 LYS B 70 0 SHEET 2 G 8 GLY B 74 VAL B 81 -1 O TYR B 76 N ARG B 68 SHEET 3 G 8 GLN B 86 ASP B 93 -1 O ILE B 90 N VAL B 77 SHEET 4 G 8 GLY B 178 GLY B 181 1 O LEU B 180 N LEU B 91 SHEET 5 G 8 PHE B 99 GLY B 102 -1 N ALA B 100 O ILE B 179 SHEET 6 G 8 THR B 155 ASP B 167 1 O ILE B 163 N VAL B 101 SHEET 7 G 8 GLY B 135 SER B 147 -1 N GLU B 138 O GLU B 165 SHEET 8 G 8 ARG B 122 TYR B 132 -1 N LYS B 126 O LEU B 141 SHEET 1 H 4 LEU B 67 LYS B 70 0 SHEET 2 H 4 GLY B 74 VAL B 81 -1 O TYR B 76 N ARG B 68 SHEET 3 H 4 GLY B 135 SER B 147 -1 O SER B 147 N THR B 80 SHEET 4 H 4 ARG B 122 TYR B 132 -1 N LYS B 126 O LEU B 141 SHEET 1 I 5 GLY B 233 ILE B 237 0 SHEET 2 I 5 PHE B 211 LEU B 215 -1 N GLN B 214 O SER B 234 SHEET 3 I 5 PHE B 402 ASP B 407 -1 O PHE B 406 N PHE B 211 SHEET 4 I 5 ARG B 412 SER B 418 -1 O ALA B 416 N TYR B 403 SHEET 5 I 5 TYR B 245 PRO B 253 -1 N THR B 252 O ILE B 413 SHEET 1 J 5 GLU B 261 VAL B 262 0 SHEET 2 J 5 SER B 286 VAL B 288 -1 O SER B 286 N VAL B 262 SHEET 3 J 5 THR B 392 MET B 394 1 O MET B 394 N ILE B 287 SHEET 4 J 5 LEU B 295 PRO B 298 -1 N ARG B 296 O VAL B 393 SHEET 5 J 5 ILE B 385 SER B 388 1 O SER B 386 N LEU B 297 SHEET 1 K 5 GLN B 272 ASP B 273 0 SHEET 2 K 5 ILE B 264 ILE B 269 -1 N ILE B 269 O GLN B 272 SHEET 3 K 5 ILE B 344 MET B 349 -1 O TYR B 347 N ARG B 266 SHEET 4 K 5 GLN B 355 ILE B 361 -1 O ILE B 361 N ILE B 344 SHEET 5 K 5 ALA B 430 VAL B 436 -1 O GLU B 432 N ARG B 358 SHEET 1 L 3 VAL B 329 TRP B 331 0 SHEET 2 L 3 ASP B 379 PHE B 383 -1 O ASP B 379 N TRP B 331 SHEET 3 L 3 LEU B 367 VAL B 370 -1 N ARG B 368 O LYS B 382 SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.08 SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.04 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.06 SSBOND 4 CYS B 216 CYS B 420 1555 1555 2.09 SSBOND 5 CYS B 278 CYS B 443 1555 1555 2.04 SSBOND 6 CYS B 330 CYS B 380 1555 1555 2.06 CISPEP 1 SER A 83 PRO A 84 0 -0.47 CISPEP 2 ARG A 189 PRO A 190 0 4.13 CISPEP 3 TYR A 283 ASP A 284 0 2.82 CISPEP 4 GLY A 433 PRO A 434 0 -3.59 CISPEP 5 SER B 83 PRO B 84 0 -3.33 CISPEP 6 ARG B 189 PRO B 190 0 5.39 CISPEP 7 TYR B 283 ASP B 284 0 1.83 CISPEP 8 GLY B 433 PRO B 434 0 -3.05 SITE 1 AC1 15 SER A 71 GLN A 73 GLY A 74 ASP A 93 SITE 2 AC1 15 TYR A 132 GLN A 134 GLY A 135 PHE A 169 SITE 3 AC1 15 TRP A 176 ASP A 289 SER A 290 GLY A 291 SITE 4 AC1 15 THR A 292 ALA A 396 HOH A1022 SITE 1 AC2 16 SER B 71 GLN B 73 GLY B 74 ASP B 93 SITE 2 AC2 16 TYR B 132 GLN B 134 GLY B 135 PHE B 169 SITE 3 AC2 16 TRP B 176 ASP B 289 SER B 290 GLY B 291 SITE 4 AC2 16 THR B 292 ALA B 396 HOH B 899 HOH B 993 CRYST1 86.473 89.495 131.427 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011564 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007609 0.00000