HEADER HYDROLASE/HYDROLASE INHIBITOR 16-NOV-12 4I0D TITLE DESIGN AND SYNTHESIS OF THIOPHENE DIHYDROISOQUINOLINS AS NOVEL BACE-1 TITLE 2 INHIBITORS CAVEAT 4I0D A HIS 423 CA HAS CHIRALITY NOT CORRESPONDING TO THE AMINO CAVEAT 2 4I0D ACID DEFINITION. SOME CLOSE CONTACTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 57-453; 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 GENE: BACE1, BACE, KIAA1149 KEYWDS BACE, ASPARTIC PROTEASE, HYDROLYSIS, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.YAO,E.BRECHT REVDAT 1 09-OCT-13 4I0D 0 JRNL AUTH Y.Z.XU,S.YUAN,S.BOWERS,R.K.HOM,W.CHAN,H.L.SHAM,Y.L.ZHU, JRNL AUTH 2 P.BEROZA,H.PAN,E.BRECHT,N.YAO,J.LOUGHEED,J.YAN,D.TAM,Z.REN, JRNL AUTH 3 L.RUSLIM,M.P.BOVA,D.R.ARTIS JRNL TITL DESIGN AND SYNTHESIS OF THIOPHENE DIHYDROISOQUINOLINES AS JRNL TITL 2 NOVEL BACE1 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 23 3075 2013 JRNL REFN ISSN 0960-894X JRNL PMID 23570791 JRNL DOI 10.1016/J.BMCL.2013.03.009 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 28240 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1495 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1642 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3063 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : -0.78000 REMARK 3 B33 (A**2) : 1.40000 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): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.854 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3176 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4321 ; 1.958 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 8.599 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;34.818 ;23.758 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;15.819 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.537 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.169 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2453 ; 0.010 ; 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): 1920 ; 1.249 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3109 ; 2.105 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1256 ; 3.199 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1212 ; 4.874 ; 4.500 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 REMARK 4 REMARK 4 4I0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-12. REMARK 100 THE RCSB ID CODE IS RCSB076145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 MICROMAX-007 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BACE-1 WAS CONCENTRATED TO 10MG/ML IN REMARK 280 100 MM BORATE PH 8.5, 9% PEG 8000, 100MM SODIUM ACETATE, 10MM REMARK 280 ZNCL2., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.00200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.00200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.57800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.81450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.57800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.81450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.00200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.57800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.81450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.00200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.57800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.81450 REMARK 290 SMTRY3 8 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -190.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.00200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 674 LIES ON A SPECIAL POSITION. 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 MET A 56 REMARK 465 ARG A 57 REMARK 465 GLY A 58 REMARK 465 SER A 59 REMARK 465 ALA A 218 REMARK 465 GLY A 219 REMARK 465 PHE A 220 REMARK 465 PRO A 221 REMARK 465 LEU A 222 REMARK 465 ASN A 223 REMARK 465 GLN A 224 REMARK 465 SER A 225 REMARK 465 GLU A 226 REMARK 465 VAL A 227 REMARK 465 LEU A 228 REMARK 465 ALA A 229 REMARK 465 SER A 230 REMARK 465 VAL A 231 REMARK 465 HIS A 461 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 O HOH A 615 O HOH A 883 1.30 REMARK 500 O HOH A 681 O HOH A 967 1.35 REMARK 500 O HOH A 815 O HOH A 951 1.54 REMARK 500 O HOH A 949 O HOH A 966 1.64 REMARK 500 O HOH A 604 O HOH A 953 1.65 REMARK 500 O HOH A 849 O HOH A 953 1.65 REMARK 500 O HOH A 956 O HOH A 977 1.83 REMARK 500 O TYR A 113 O HOH A 967 1.85 REMARK 500 CE1 HIS A 460 O HOH A 932 1.89 REMARK 500 OE1 GLU A 165 O HOH A 850 1.94 REMARK 500 O HOH A 678 O HOH A 892 1.99 REMARK 500 O HOH A 831 O HOH A 875 2.00 REMARK 500 CD2 HIS A 423 O HOH A 626 2.03 REMARK 500 OE1 GLU A 441 O HOH A 797 2.03 REMARK 500 O HOH A 847 O HOH A 969 2.07 REMARK 500 O HOH A 816 O HOH A 955 2.15 REMARK 500 O HOH A 730 O HOH A 883 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 863 O HOH A 945 5555 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 281 CE2 TYR A 281 CD2 0.096 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 210 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP A 277 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 284 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU A 438 CA - CB - CG ANGL. DEV. = 23.1 DEGREES 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 103 18.67 -140.90 REMARK 500 HIS A 150 46.61 -105.96 REMARK 500 PHE A 169 -62.07 -106.04 REMARK 500 ASN A 175 11.32 80.05 REMARK 500 HIS A 206 25.26 45.88 REMARK 500 TRP A 258 -87.27 -141.68 REMARK 500 ASN A 270 68.42 21.88 REMARK 500 THR A 375 42.92 -82.32 REMARK 500 ASP A 439 -106.07 -90.80 REMARK 500 GLU A 441 116.65 57.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 258 TYR A 259 148.32 REMARK 500 MET A 440 GLU A 441 61.46 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 HIS A 423 5.2 L L EXPECTING SP3 REMARK 500 ASP A 439 24.4 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 A 832 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 939 DISTANCE = 5.74 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 459 NE2 REMARK 620 2 HIS A 457 ND1 118.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 932 O REMARK 620 2 HOH A 625 O 150.5 REMARK 620 3 HIS A 458 ND1 73.5 122.0 REMARK 620 4 ASP A 192 OD1 112.0 77.6 132.0 REMARK 620 5 ASP A 192 OD2 62.7 133.2 93.3 55.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 150 NE2 REMARK 620 2 HOH A 922 O 93.1 REMARK 620 3 GLU A 78 OE2 94.5 163.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1B7 A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HZT RELATED DB: PDB REMARK 900 RELATED ID: 4I0E RELATED DB: PDB REMARK 900 RELATED ID: 4I0F RELATED DB: PDB REMARK 900 RELATED ID: 4I0G RELATED DB: PDB REMARK 900 RELATED ID: 4I0Z RELATED DB: PDB REMARK 900 RELATED ID: 4I10 RELATED DB: PDB REMARK 900 RELATED ID: 4I12 RELATED DB: PDB REMARK 900 RELATED ID: 4I1C RELATED DB: PDB DBREF 4I0D A 57 453 UNP P56817 BACE1_HUMAN 57 453 SEQADV 4I0D MET A 56 UNP P56817 EXPRESSION TAG SEQADV 4I0D ARG A 454 UNP P56817 EXPRESSION TAG SEQADV 4I0D SER A 455 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 456 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 457 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 458 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 459 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 460 UNP P56817 EXPRESSION TAG SEQADV 4I0D HIS A 461 UNP P56817 EXPRESSION TAG SEQRES 1 A 406 MET ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG SEQRES 2 A 406 GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL SEQRES 3 A 406 GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR SEQRES 4 A 406 GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO SEQRES 5 A 406 PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR SEQRES 6 A 406 TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR SEQRES 7 A 406 GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SEQRES 8 A 406 SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN SEQRES 9 A 406 ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN SEQRES 10 A 406 GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA SEQRES 11 A 406 GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE SEQRES 12 A 406 ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SEQRES 13 A 406 SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SEQRES 14 A 406 SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE SEQRES 15 A 406 GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP SEQRES 16 A 406 TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE SEQRES 17 A 406 ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET SEQRES 18 A 406 ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SEQRES 19 A 406 SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE SEQRES 20 A 406 GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER THR SEQRES 21 A 406 GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU SEQRES 22 A 406 VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE SEQRES 23 A 406 PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN SEQRES 24 A 406 GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU SEQRES 25 A 406 ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS SEQRES 26 A 406 TYR LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL SEQRES 27 A 406 MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE SEQRES 28 A 406 ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA SEQRES 29 A 406 CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU SEQRES 30 A 406 GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR SEQRES 31 A 406 ASN ILE PRO GLN THR ASP GLU SER ARG SER HIS HIS HIS SEQRES 32 A 406 HIS HIS HIS HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET 1B7 A 504 27 HETNAM ZN ZINC ION HETNAM 1B7 N-(6-CHLORO-3,3-DIMETHYL-3,4-DIHYDROISOQUINOLIN-1-YL)- HETNAM 2 1B7 3-(4-PROPYLTHIOPHEN-3-YL)-L-ALANINE FORMUL 2 ZN 3(ZN 2+) FORMUL 5 1B7 C21 H25 CL N2 O2 S FORMUL 6 HOH *380(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 HIS A 206 1 11 HELIX 4 4 ASP A 241 SER A 243 5 3 HELIX 5 5 ASP A 277 TYR A 283 5 7 HELIX 6 6 LYS A 299 SER A 313 1 15 HELIX 7 7 PRO A 319 LEU A 324 1 6 HELIX 8 8 PRO A 337 PHE A 341 5 5 HELIX 9 9 LEU A 362 TYR A 366 1 5 HELIX 10 10 GLY A 395 GLU A 400 1 6 HELIX 11 11 THR A 450 HIS A 456 1 7 SHEET 1 A 8 LEU A 67 LYS A 70 0 SHEET 2 A 8 GLY A 74 VAL A 81 -1 O GLY A 74 N LYS A 70 SHEET 3 A 8 GLN A 86 ASP A 93 -1 O VAL A 92 N TYR A 75 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 VAL A 156 ASP A 167 1 O ILE A 163 N VAL A 101 SHEET 7 A 8 GLY A 135 SER A 147 -1 N LYS A 136 O ASP A 167 SHEET 8 A 8 ARG A 122 TYR A 132 -1 N TYR A 132 O GLY A 135 SHEET 1 B 4 LEU A 67 LYS A 70 0 SHEET 2 B 4 GLY A 74 VAL A 81 -1 O GLY A 74 N LYS A 70 SHEET 3 B 4 GLY A 135 SER A 147 -1 O SER A 147 N THR A 80 SHEET 4 B 4 ARG A 122 TYR A 132 -1 N TYR A 132 O GLY A 135 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 388 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 VAL A 265 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 ALA A 430 N THR A 360 SHEET 1 F 3 VAL A 329 GLN A 332 0 SHEET 2 F 3 ASP A 378 PHE A 383 -1 O TYR A 381 N VAL A 329 SHEET 3 F 3 LEU A 367 PRO A 369 -1 N ARG A 368 O LYS A 382 SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.04 SSBOND 2 CYS A 278 CYS A 443 1555 1555 1.98 SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.04 LINK NE2 HIS A 459 ZN ZN A 501 1555 1555 1.92 LINK ZN ZN A 502 O HOH A 932 1555 1555 1.97 LINK ND1 HIS A 457 ZN ZN A 501 1555 1555 2.04 LINK ZN ZN A 502 O HOH A 625 1555 1555 2.07 LINK ND1 HIS A 458 ZN ZN A 502 1555 1555 2.11 LINK NE2 HIS A 150 ZN ZN A 503 1555 1555 2.12 LINK ZN ZN A 503 O HOH A 922 1555 1555 2.25 LINK OD1 ASP A 192 ZN ZN A 502 1555 1555 2.26 LINK OE2 GLU A 78 ZN ZN A 503 1555 1555 2.27 LINK OD2 ASP A 192 ZN ZN A 502 1555 1555 2.42 CISPEP 1 SER A 83 PRO A 84 0 -0.01 CISPEP 2 ARG A 189 PRO A 190 0 2.63 CISPEP 3 TYR A 283 ASP A 284 0 10.57 CISPEP 4 GLY A 433 PRO A 434 0 -2.80 CISPEP 5 ASP A 439 MET A 440 0 -22.76 SITE 1 AC1 5 GLU A 316 TRP A 331 ASP A 451 HIS A 457 SITE 2 AC1 5 HIS A 459 SITE 1 AC2 5 ASP A 192 HIS A 458 HIS A 460 HOH A 625 SITE 2 AC2 5 HOH A 932 SITE 1 AC3 4 GLU A 78 HIS A 110 HIS A 150 HOH A 922 SITE 1 AC4 20 SER A 71 GLN A 73 GLY A 74 LEU A 91 SITE 2 AC4 20 ASP A 93 TYR A 132 GLN A 134 GLY A 135 SITE 3 AC4 20 LYS A 136 LYS A 168 PHE A 169 ILE A 171 SITE 4 AC4 20 SER A 290 GLY A 291 THR A 292 THR A 293 SITE 5 AC4 20 HOH A 619 HOH A 810 HOH A 852 HOH A 869 CRYST1 75.156 103.629 100.004 90.00 90.00 90.00 C 2 2 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 0.013306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010000 0.00000