HEADER HYDROLASE 05-FEB-08 2VNM TITLE HUMAN BACE-1 IN COMPLEX WITH 3-(1,1-DIOXIDOTETRAHYDRO-2H-1,2-THIAZIN- TITLE 2 2-YL)-5-(ETHYLAMINO)-N-((1S,2R)-2-HYDROXY-1-(PHENYLMETHYL)-3-(((3- TITLE 3 (TRIFLUOROMETHYL)PHENYL)METHYL)AMINO)PROPYL)BENZAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 61-452; COMPND 5 SYNONYM: BACE-1, BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID COMPND 6 PRECURSOR PROTEIN CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC COMPND 7 PROTEASE 2, MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; COMPND 8 EC: 3.4.23.46; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: 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: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: CHO KEYWDS HYDROLASE, ALTERNATIVE SPLICING, BETA-SITE APP CLEAVING ENZYME, BETA- KEYWDS 2 SECRETASE, ASPARTYL PROTEASE, ASP-2, BACE-1, ZYMOGEN, PROTEASE, KEYWDS 3 MEMBRANE, MEMAPSIN-2, GLYCOPROTEIN, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR N.CHARRIER,B.CLARKE,L.CUTLER,E.DEMONT,C.DINGWALL,R.DUNSDON,P.EAST, AUTHOR 2 J.HAWKINS,C.HOWES,I.HUSSAIN,P.JEFFREY,G.MAILE,R.MATICO,J.MOSLEY, AUTHOR 3 A.NAYLOR,A.OBRIEN,S.REDSHAW,P.ROWLAND,V.SOLEIL,K.J.SMITH,S.SWEITZER, AUTHOR 4 P.THEOBALD,D.VESEY,D.S.WALTER,G.WAYNE REVDAT 6 15-MAY-19 2VNM 1 REMARK REVDAT 5 03-APR-19 2VNM 1 SOURCE REVDAT 4 06-MAR-19 2VNM 1 REMARK REVDAT 3 24-FEB-09 2VNM 1 VERSN REVDAT 2 17-JUN-08 2VNM 1 JRNL REVDAT 1 20-MAY-08 2VNM 0 JRNL AUTH N.CHARRIER,B.CLARKE,L.CUTLER,E.DEMONT,C.DINGWALL,R.DUNSDON, JRNL AUTH 2 P.EAST,J.HAWKINS,C.HOWES,I.HUSSAIN,P.JEFFREY,G.MAILE, JRNL AUTH 3 R.MATICO,J.MOSLEY,A.NAYLOR,A.O'BRIEN,S.REDSHAW,P.ROWLAND, JRNL AUTH 4 V.SOLEIL,K.J.SMITH,S.SWEITZER,P.THEOBALD,D.VESEY,D.S.WALTER, JRNL AUTH 5 G.WAYNE JRNL TITL SECOND GENERATION OF HYDROXYETHYLAMINE BACE-1 INHIBITORS: JRNL TITL 2 OPTIMIZING POTENCY AND ORAL BIOAVAILABILITY. JRNL REF J.MED.CHEM. V. 51 3313 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18457381 JRNL DOI 10.1021/JM800138H REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0006 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 35018 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2585 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 366 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.43000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : -1.23000 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.623 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3121 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4259 ; 1.361 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1944 ; 0.934 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3082 ; 1.479 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1363 ; 2.210 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1177 ; 3.435 ; 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. TWO MOLECULES OF THE LIGAND SEEN IN THIS STRUCTURE, REMARK 3 ONE IN THE ACTIVE SITE AND ONE BETWEEN CRYSTAL CONTACTS. REMARK 4 REMARK 4 2VNM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0723 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 201388 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GROWN BY VAPOUR DIFFUSION AT REMARK 280 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH REMARK 280 3.2, VAPOR DIFFUSION, TEMPERATURE 293K 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 23.97600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.24600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.24600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.97600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.10850 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 223 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 354 TO GLN 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 VAL A 61 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 GLN 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 PRO A 448 REMARK 465 GLN A 449 REMARK 465 THR A 450 REMARK 465 ASP A 451 REMARK 465 GLU A 452 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 LEU A 438 CG CD1 CD2 REMARK 470 ILE A 447 CA C O CB CG1 CG2 CD1 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 PHE A 169 -65.10 -96.89 REMARK 500 TRP A 258 -86.82 -140.99 REMARK 500 ASP A 372 116.55 -161.63 REMARK 500 ASP A 372 117.14 -161.63 REMARK 500 ALA A 384 34.23 -95.35 REMARK 500 ASP A 424 -158.95 -123.01 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 CM8 A2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM8 A2001 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 1M4H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BETA-SECRETASE COMPLEXED WITHINHIBITOR OM00-3 REMARK 900 RELATED ID: 1XN2 RELATED DB: PDB REMARK 900 NEW SUBSTRATE BINDING POCKETS FOR BETA- SECRETASE. 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: 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- REMARK 900 1-YL)BENZAMIDE 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: 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: 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: 2B8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH L-000384950 REMARK 900 RELATED ID: 1YM4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AMK640 REMARK 900 RELATED ID: 1SGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE CATALYTICDOMAIN. 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: 1UJK RELATED DB: PDB REMARK 900 VHS DOMAIN OF HUMAN GGA1 COMPLEXED WITH C -TERMINALPHOSPHOPEPTIDE REMARK 900 FROM BACE 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: 1FKN RELATED DB: PDB REMARK 900 STRUCTURE OF BETA-SECRETASE COMPLEXED WITH INHIBITOR 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: 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: 2VA7 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 27 REMARK 900 RELATED ID: 1YM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITHNVP-AUR200 REMARK 900 RELATED ID: 2VKM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GRL-8234 BOUND TO BACE (BETA-SECRETASE) 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: 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: 1PY1 RELATED DB: PDB REMARK 900 COMPLEX OF GGA1-VHS DOMAIN AND BETA- SECRETASE C- REMARK 900 TERMINALPHOSPHOPEPTIDE REMARK 900 RELATED ID: 1W50 RELATED DB: PDB REMARK 900 APO STRUCTURE OF BACE (BETA SECRETASE) 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: 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: 1W51 RELATED DB: PDB REMARK 900 BACE (BETA SECRETASE) IN COMPLEX WITH A NANOMOLAR NON-PEPTIDIC REMARK 900 INHIBITOR DBREF 2VNM A 61 452 UNP P56817 BACE1_HUMAN 61 452 SEQADV 2VNM GLN A 153 UNP P56817 ASN 153 ENGINEERED MUTATION SEQADV 2VNM GLN A 172 UNP P56817 ASN 172 ENGINEERED MUTATION SEQADV 2VNM GLN A 223 UNP P56817 ASN 223 ENGINEERED MUTATION SEQADV 2VNM GLN A 354 UNP P56817 ASN 354 ENGINEERED MUTATION SEQRES 1 A 392 VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SER GLY GLN SEQRES 2 A 392 GLY TYR TYR VAL GLU MET THR VAL GLY SER PRO PRO GLN SEQRES 3 A 392 THR LEU ASN ILE LEU VAL ASP THR GLY SER SER ASN PHE SEQRES 4 A 392 ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU HIS ARG TYR SEQRES 5 A 392 TYR GLN ARG GLN LEU SER SER THR TYR ARG ASP LEU ARG SEQRES 6 A 392 LYS GLY VAL TYR VAL PRO TYR THR GLN GLY LYS TRP GLU SEQRES 7 A 392 GLY GLU LEU GLY THR ASP LEU VAL SER ILE PRO HIS GLY SEQRES 8 A 392 PRO GLN VAL THR VAL ARG ALA ASN ILE ALA ALA ILE THR SEQRES 9 A 392 GLU SER ASP LYS PHE PHE ILE GLN GLY SER ASN TRP GLU SEQRES 10 A 392 GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE ALA ARG PRO SEQRES 11 A 392 ASP ASP SER LEU GLU PRO PHE PHE ASP SER LEU VAL LYS SEQRES 12 A 392 GLN THR HIS VAL PRO ASN LEU PHE SER LEU GLN LEU CYS SEQRES 13 A 392 GLY ALA GLY PHE PRO LEU GLN GLN SER GLU VAL LEU ALA SEQRES 14 A 392 SER VAL GLY GLY SER MET ILE ILE GLY GLY ILE ASP HIS SEQRES 15 A 392 SER LEU TYR THR GLY SER LEU TRP TYR THR PRO ILE ARG SEQRES 16 A 392 ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL ARG VAL GLU SEQRES 17 A 392 ILE ASN GLY GLN ASP LEU LYS MET ASP CYS LYS GLU TYR SEQRES 18 A 392 ASN TYR ASP LYS SER ILE VAL ASP SER GLY THR THR ASN SEQRES 19 A 392 LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA ALA VAL LYS SEQRES 20 A 392 SER ILE LYS ALA ALA SER SER THR GLU LYS PHE PRO ASP SEQRES 21 A 392 GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS TRP GLN ALA SEQRES 22 A 392 GLY THR THR PRO TRP ASN ILE PHE PRO VAL ILE SER LEU SEQRES 23 A 392 TYR LEU MET GLY GLU VAL THR GLN GLN SER PHE ARG ILE SEQRES 24 A 392 THR ILE LEU PRO GLN GLN TYR LEU ARG PRO VAL GLU ASP SEQRES 25 A 392 VAL ALA THR SER GLN ASP ASP CYS TYR LYS PHE ALA ILE SEQRES 26 A 392 SER GLN SER SER THR GLY THR VAL MET GLY ALA VAL ILE SEQRES 27 A 392 MET GLU GLY PHE TYR VAL VAL PHE ASP ARG ALA ARG LYS SEQRES 28 A 392 ARG ILE GLY PHE ALA VAL SER ALA CYS HIS VAL HIS ASP SEQRES 29 A 392 GLU PHE ARG THR ALA ALA VAL GLU GLY PRO PHE VAL THR SEQRES 30 A 392 LEU ASP MET GLU ASP CYS GLY TYR ASN ILE PRO GLN THR SEQRES 31 A 392 ASP GLU HET CM8 A2000 43 HET CM8 A2001 43 HETNAM CM8 N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{[3-(TRIFLUOROMETHYL) HETNAM 2 CM8 BENZYL]AMINO}PROPYL]-3-(1,1-DIOXIDO-1,2-THIAZINAN-2- HETNAM 3 CM8 YL)-5-(ETHYLAMINO)BENZAMIDE FORMUL 2 CM8 2(C31 H37 F3 N4 O4 S) FORMUL 4 HOH *366(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 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 ASP A 372 SER A 376 5 5 HELIX 11 11 GLY A 395 GLU A 400 1 6 HELIX 12 12 ARG A 408 ARG A 410 5 3 SHEET 1 AA 3 ARG A 122 PRO A 131 0 SHEET 2 AA 3 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130 SHEET 3 AA 3 TYR A 75 VAL A 81 -1 O THR A 80 N SER A 147 SHEET 1 AB 7 ARG A 122 PRO A 131 0 SHEET 2 AB 7 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130 SHEET 3 AB 7 THR A 155 ASP A 167 -1 O VAL A 156 N VAL A 146 SHEET 4 AB 7 PHE A 99 GLY A 102 1 O PHE A 99 N ALA A 161 SHEET 5 AB 7 GLY A 178 GLY A 181 -1 O ILE A 179 N ALA A 100 SHEET 6 AB 7 GLN A 86 ASP A 93 1 O LEU A 91 N LEU A 180 SHEET 7 AB 7 TYR A 75 VAL A 81 -1 O TYR A 75 N VAL A 92 SHEET 1 AC 5 GLU A 261 VAL A 262 0 SHEET 2 AC 5 SER A 286 VAL A 288 -1 O SER A 286 N VAL A 262 SHEET 3 AC 5 THR A 392 MET A 394 1 O THR A 392 N ILE A 287 SHEET 4 AC 5 LEU A 295 PRO A 298 -1 O ARG A 296 N VAL A 393 SHEET 5 AC 5 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297 SHEET 1 AD 5 GLN A 272 ASP A 273 0 SHEET 2 AD 5 ILE A 264 ILE A 269 -1 O ILE A 269 N GLN A 272 SHEET 3 AD 5 ILE A 344 MET A 349 -1 O SER A 345 N GLU A 268 SHEET 4 AD 5 GLN A 355 ILE A 361 -1 O PHE A 357 N LEU A 348 SHEET 5 AD 5 ALA A 430 VAL A 436 -1 O ALA A 430 N THR A 360 SHEET 1 AE 3 VAL A 329 GLN A 332 0 SHEET 2 AE 3 ASP A 378 PHE A 383 -1 O ASP A 379 N TRP A 331 SHEET 3 AE 3 LEU A 367 PRO A 369 -1 O ARG A 368 N LYS A 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 2.08 CISPEP 1 SER A 83 PRO A 84 0 -2.61 CISPEP 2 ARG A 189 PRO A 190 0 1.79 CISPEP 3 TYR A 283 ASP A 284 0 2.62 CISPEP 4 GLY A 433 PRO A 434 0 -4.01 SITE 1 AC1 20 LEU A 91 ASP A 93 GLY A 95 SER A 96 SITE 2 AC1 20 PRO A 131 TYR A 132 THR A 133 GLN A 134 SITE 3 AC1 20 PHE A 169 TRP A 176 ILE A 179 ARG A 189 SITE 4 AC1 20 TYR A 259 ASP A 289 GLY A 291 THR A 292 SITE 5 AC1 20 THR A 293 ASN A 294 ARG A 296 SER A 386 SITE 1 AC2 16 SER A 83 THR A 155 GLN A 204 ASN A 270 SITE 2 AC2 16 GLY A 271 ASN A 339 VAL A 343 ALA A 374 SITE 3 AC2 16 PHE A 426 ARG A 427 THR A 428 ALA A 430 SITE 4 AC2 16 GLU A 432 HOH A2210 HOH A2316 HOH A2366 CRYST1 47.952 76.217 104.492 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 0.020854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009570 0.00000