4NWL - Header Asymmetric Unit

HEADER HYDROLASE/HYDROLASE INHIBITOR 06-DEC-13 4NWL

TITLE CRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TITLE 2 BMS-650032 AKA N-(TERT-BUTOXYCARBONYL)-3-ME THYL-L-VALYL-(4R)-4-((7- TITLE 3 CHLORO-4-METHOXY-1-ISOQUINOLINYL)O XY)-N-((1R,2S)-1- TITLE 4 ((CYCLOPROPYLSULFONYL)CARBAMOYL)-2-VINYLC YCLOPROPYL)-L-PROLINAMIDE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCV NS3 1A PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE PROTEIN CRYSTALLIZED IS A SINGLE-CHAIN CONSTRUCT COMPND 6 OF PROTEASE DOMAIN OF HEPATITIS C VIRUS NS3/4A, WITH COFACTOR 4A COMPND 7 COVALENTLY LINKED AT THE N-TERMINUS.

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_TAXID: 31646; SOURCE 4 STRAIN: 1A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562

KEYWDS HYDROLASE/HYDROLASE INHIBITOR, SERINE PROTEASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX

EXPDTA X-RAY DIFFRACTION

AUTHOR J.K.MUCKELBAUER,H.E.KLEI

REVDAT 2 25-NOV-15 4NWL 1 HETSYN REMARK REVDAT 1 26-MAR-14 4NWL 0

JRNL AUTH P.M.SCOLA,A.X.WANG,A.C.GOOD,L.Q.SUN,K.D.COMBRINK, JRNL AUTH 2 J.A.CAMPBELL,J.CHEN,Y.TU,N.SIN,B.L.VENABLES,S.Y.SIT,Y.CHEN, JRNL AUTH 3 A.COCUZZA,D.M.BILDER,S.D'ANDREA,B.ZHENG,P.HEWAWASAM,M.DING, JRNL AUTH 4 J.THURING,J.LI,D.HERNANDEZ,F.YU,P.FALK,G.ZHAI,A.K.SHEAFFER, JRNL AUTH 5 C.CHEN,M.S.LEE,D.BARRY,J.O.KNIPE,W.LI,Y.H.HAN,S.JENKINS, JRNL AUTH 6 C.GESENBERG,Q.GAO,M.W.SINZ,K.S.SANTONE,T.ZVYAGA,R.RAJAMANI, JRNL AUTH 7 H.E.KLEI,R.J.COLONNO,D.M.GRASELA,E.HUGHES,C.CHIEN,S.ADAMS, JRNL AUTH 8 P.C.LEVESQUE,D.LI,J.ZHU,N.A.MEANWELL,F.MCPHEE JRNL TITL DISCOVERY AND EARLY CLINICAL EVALUATION OF BMS-605339, A JRNL TITL 2 POTENT AND ORALLY EFFICACIOUS TRIPEPTIDIC ACYLSULFONAMIDE JRNL TITL 3 NS3 PROTEASE INHIBITOR FOR THE TREATMENT OF HEPATITIS C JRNL TITL 4 VIRUS INFECTION. JRNL REF J.MED.CHEM. V. 57 1708 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 24555570 JRNL DOI 10.1021/JM401840S

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.E.KLEI,K.KISH,M.F.RUSSO,S.J.MICHALCZYK,M.H.CAHN,J.TREDUP, REMARK 1 AUTH 2 C.CHANG,J.KHAN,E.T.BALDWIN REMARK 1 TITL IMAGE ANNOTATION AND DATABASE MINING TO CREATE A NOVEL REMARK 1 TITL 2 SCREEN FOR THE CHEMOTYPE-DEPENDENT CRYSTALLIZATION OF HCV REMARK 1 TITL 3 NS3 PROTEASE REMARK 1 REF CRYST.GROWTH DES. V. 11 1143 2011 REMARK 1 REFN ISSN 1528-7483 REMARK 1 DOI 10.1021/CG101353H

REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1162918.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 17845 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) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 623 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2480 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2460 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 623 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0120 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17845 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2053 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 69 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2876 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.28000 REMARK 3 B22 (A**2) : -2.86000 REMARK 3 B33 (A**2) : -5.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 3.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.200 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.520 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.760 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.390 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 40.68 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARA REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARA REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : LIGAND.PARAM REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 4NWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB083746.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17859 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.06000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 17.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.88050 REMARK 290 SMTRY3 2 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 MET A -14 REMARK 465 LYS A -13 REMARK 465 LYS A -12 REMARK 465 ALA A 183 REMARK 465 ILE A 184 REMARK 465 ARG A 185 REMARK 465 ALA A 186 REMARK 465 PRO A 187 REMARK 465 SER A 188 REMARK 465 THR A 189 REMARK 465 SER A 190 REMARK 465 LEU A 191 REMARK 465 ARG A 192 REMARK 465 PRO A 193 REMARK 465 HIS A 194 REMARK 465 SER A 195 REMARK 465 SER A 196 REMARK 465 THR A 197 REMARK 465 THR A 198 REMARK 465 THR A 199 REMARK 465 THR A 200 REMARK 465 THR A 201 REMARK 465 THR A 202 REMARK 465 GLU A 203 REMARK 465 ILE A 204 REMARK 465 MET B -14 REMARK 465 LYS B -13 REMARK 465 LYS B -12 REMARK 465 ALA B 183 REMARK 465 ILE B 184 REMARK 465 ARG B 185 REMARK 465 ALA B 186 REMARK 465 PRO B 187 REMARK 465 SER B 188 REMARK 465 THR B 189 REMARK 465 SER B 190 REMARK 465 LEU B 191 REMARK 465 ARG B 192 REMARK 465 PRO B 193 REMARK 465 HIS B 194 REMARK 465 SER B 195 REMARK 465 SER B 196 REMARK 465 THR B 197 REMARK 465 THR B 198 REMARK 465 THR B 199 REMARK 465 THR B 200 REMARK 465 THR B 201 REMARK 465 THR B 202 REMARK 465 GLU B 203 REMARK 465 ILE B 204

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 PRO A 182 O REMARK 470 PRO B 182 O

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 GLU A 13 39.81 -80.11 REMARK 500 GLU A 14 -38.03 -133.02 REMARK 500 THR A 38 -165.28 -109.46 REMARK 500 ALA A 111 19.78 53.91 REMARK 500 THR B 38 -165.79 -107.23 REMARK 500 REMARK 500 REMARK: NULL

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 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 CYS A 97 SG 111.0 REMARK 620 3 HIS A 149 ND1 100.2 127.2 REMARK 620 4 CYS A 145 SG 120.1 106.8 91.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 149 ND1 REMARK 620 2 CYS B 97 SG 127.2 REMARK 620 3 CYS B 145 SG 91.2 104.5 REMARK 620 4 CYS B 99 SG 102.3 106.4 127.4 REMARK 620 N 1 2 3

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2R9 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2R9 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NWK RELATED DB: PDB

REMARK 999 REMARK 999 SEQUENCE REMARK 999 The cofactor 4A residues -10-0(GLY SER VAL VAL ILE VAL GLY ARG ILE REMARK 999 ASN LEU) in this entry correspond to residues numbering 1678-1688 REMARK 999 of database sequence reference (UNP A8DG50). This peptide is REMARK 999 covalently linked to the N-terminus of NS3 via LINKER (SER GLY ASP REMARK 999 THR). C1679S mutation was engineered to prevent disulfide REMARK 999 formation. The V1686I and I1687N were engineered to optimize the REMARK 999 linker between the cofactor 4A and NS3.

DBREF 4NWL A -10 0 UNP A8DG50 A8DG50_9HEPC 1678 1688 DBREF 4NWL A 5 182 UNP A8DG50 A8DG50_9HEPC 1035 1212 DBREF 4NWL B -10 0 UNP A8DG50 A8DG50_9HEPC 1678 1688 DBREF 4NWL B 5 182 UNP A8DG50 A8DG50_9HEPC 1035 1212

SEQADV 4NWL MET A -14 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS A -13 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS A -12 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS A -11 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER A -9 UNP A8DG50 CYS 1679 SEE REMARK 999 SEQADV 4NWL ILE A -2 UNP A8DG50 VAL 1686 SEE REMARK 999 SEQADV 4NWL ASN A -1 UNP A8DG50 ILE 1687 SEE REMARK 999 SEQADV 4NWL SER A 1 UNP A8DG50 LINKER SEQADV 4NWL GLY A 2 UNP A8DG50 LINKER SEQADV 4NWL ASP A 3 UNP A8DG50 LINKER SEQADV 4NWL THR A 4 UNP A8DG50 LINKER SEQADV 4NWL GLU A 13 UNP A8DG50 LEU 1043 ENGINEERED MUTATION SEQADV 4NWL GLU A 14 UNP A8DG50 LEU 1044 ENGINEERED MUTATION SEQADV 4NWL GLN A 17 UNP A8DG50 ILE 1047 ENGINEERED MUTATION SEQADV 4NWL GLU A 18 UNP A8DG50 ILE 1048 ENGINEERED MUTATION SEQADV 4NWL GLN A 21 UNP A8DG50 LEU 1051 ENGINEERED MUTATION SEQADV 4NWL THR A 40 UNP A8DG50 ALA 1070 ENGINEERED MUTATION SEQADV 4NWL SER A 47 UNP A8DG50 CYS 1077 ENGINEERED MUTATION SEQADV 4NWL LEU A 52 UNP A8DG50 CYS 1082 ENGINEERED MUTATION SEQADV 4NWL THR A 72 UNP A8DG50 ILE 1102 ENGINEERED MUTATION SEQADV 4NWL GLN A 86 UNP A8DG50 PRO 1116 ENGINEERED MUTATION SEQADV 4NWL ALA A 183 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ILE A 184 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ARG A 185 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ALA A 186 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL PRO A 187 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER A 188 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 189 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER A 190 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LEU A 191 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ARG A 192 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL PRO A 193 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL HIS A 194 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER A 195 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER A 196 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 197 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 198 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 199 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 200 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 201 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR A 202 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL GLU A 203 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ILE A 204 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL MET B -14 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS B -13 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS B -12 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LYS B -11 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER B -9 UNP A8DG50 CYS 1679 SEE REMARK 999 SEQADV 4NWL ILE B -2 UNP A8DG50 VAL 1686 SEE REMARK 999 SEQADV 4NWL ASN B -1 UNP A8DG50 ILE 1687 SEE REMARK 999 SEQADV 4NWL SER B 1 UNP A8DG50 LINKER SEQADV 4NWL GLY B 2 UNP A8DG50 LINKER SEQADV 4NWL ASP B 3 UNP A8DG50 LINKER SEQADV 4NWL THR B 4 UNP A8DG50 LINKER SEQADV 4NWL GLU B 13 UNP A8DG50 LEU 1043 ENGINEERED MUTATION SEQADV 4NWL GLU B 14 UNP A8DG50 LEU 1044 ENGINEERED MUTATION SEQADV 4NWL GLN B 17 UNP A8DG50 ILE 1047 ENGINEERED MUTATION SEQADV 4NWL GLU B 18 UNP A8DG50 ILE 1048 ENGINEERED MUTATION SEQADV 4NWL GLN B 21 UNP A8DG50 LEU 1051 ENGINEERED MUTATION SEQADV 4NWL THR B 40 UNP A8DG50 ALA 1070 ENGINEERED MUTATION SEQADV 4NWL SER B 47 UNP A8DG50 CYS 1077 ENGINEERED MUTATION SEQADV 4NWL LEU B 52 UNP A8DG50 CYS 1082 ENGINEERED MUTATION SEQADV 4NWL THR B 72 UNP A8DG50 ILE 1102 ENGINEERED MUTATION SEQADV 4NWL GLN B 86 UNP A8DG50 PRO 1116 ENGINEERED MUTATION SEQADV 4NWL ALA B 183 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ILE B 184 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ARG B 185 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ALA B 186 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL PRO B 187 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER B 188 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 189 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER B 190 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL LEU B 191 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ARG B 192 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL PRO B 193 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL HIS B 194 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER B 195 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL SER B 196 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 197 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 198 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 199 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 200 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 201 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL THR B 202 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL GLU B 203 UNP A8DG50 EXPRESSION TAG SEQADV 4NWL ILE B 204 UNP A8DG50 EXPRESSION TAG

SEQRES 1 A 219 MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE SEQRES 2 A 219 ASN LEU SER GLY ASP THR ALA TYR ALA GLN GLN THR ARG SEQRES 3 A 219 GLY GLU GLU GLY CYS GLN GLU THR SER GLN THR GLY ARG SEQRES 4 A 219 ASP LYS ASN GLN VAL GLU GLY GLU VAL GLN ILE VAL SER SEQRES 5 A 219 THR ALA THR GLN THR PHE LEU ALA THR SER ILE ASN GLY SEQRES 6 A 219 VAL LEU TRP THR VAL TYR HIS GLY ALA GLY THR ARG THR SEQRES 7 A 219 ILE ALA SER PRO LYS GLY PRO VAL THR GLN MET TYR THR SEQRES 8 A 219 ASN VAL ASP LYS ASP LEU VAL GLY TRP GLN ALA PRO GLN SEQRES 9 A 219 GLY SER ARG SER LEU THR PRO CYS THR CYS GLY SER SER SEQRES 10 A 219 ASP LEU TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO SEQRES 11 A 219 VAL ARG ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER SEQRES 12 A 219 PRO ARG PRO ILE SER TYR LEU LYS GLY SER SER GLY GLY SEQRES 13 A 219 PRO LEU LEU CYS PRO ALA GLY HIS ALA VAL GLY ILE PHE SEQRES 14 A 219 ARG ALA ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL SEQRES 15 A 219 ASP PHE ILE PRO VAL GLU SER LEU GLU THR THR MET ARG SEQRES 16 A 219 SER PRO ALA ILE ARG ALA PRO SER THR SER LEU ARG PRO SEQRES 17 A 219 HIS SER SER THR THR THR THR THR THR GLU ILE SEQRES 1 B 219 MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE SEQRES 2 B 219 ASN LEU SER GLY ASP THR ALA TYR ALA GLN GLN THR ARG SEQRES 3 B 219 GLY GLU GLU GLY CYS GLN GLU THR SER GLN THR GLY ARG SEQRES 4 B 219 ASP LYS ASN GLN VAL GLU GLY GLU VAL GLN ILE VAL SER SEQRES 5 B 219 THR ALA THR GLN THR PHE LEU ALA THR SER ILE ASN GLY SEQRES 6 B 219 VAL LEU TRP THR VAL TYR HIS GLY ALA GLY THR ARG THR SEQRES 7 B 219 ILE ALA SER PRO LYS GLY PRO VAL THR GLN MET TYR THR SEQRES 8 B 219 ASN VAL ASP LYS ASP LEU VAL GLY TRP GLN ALA PRO GLN SEQRES 9 B 219 GLY SER ARG SER LEU THR PRO CYS THR CYS GLY SER SER SEQRES 10 B 219 ASP LEU TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO SEQRES 11 B 219 VAL ARG ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER SEQRES 12 B 219 PRO ARG PRO ILE SER TYR LEU LYS GLY SER SER GLY GLY SEQRES 13 B 219 PRO LEU LEU CYS PRO ALA GLY HIS ALA VAL GLY ILE PHE SEQRES 14 B 219 ARG ALA ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL SEQRES 15 B 219 ASP PHE ILE PRO VAL GLU SER LEU GLU THR THR MET ARG SEQRES 16 B 219 SER PRO ALA ILE ARG ALA PRO SER THR SER LEU ARG PRO SEQRES 17 B 219 HIS SER SER THR THR THR THR THR THR GLU ILE

HET 2R9 A 301 51 HET ZN A 302 1 HET 2R9 B 301 51 HET ZN B 302 1

HETNAM 2R9 N-(TERT-BUTOXYCARBONYL)-3-METHYL-L-VALYL-(4R)-4-[(7- HETNAM 2 2R9 CHLORO-4-METHOXYISOQUINOLIN-1-YL)OXY]-N-{(1R,2S)-1- HETNAM 3 2R9 [(CYCLOPROPYLSULFONYL)CARBAMOYL]-2- HETNAM 4 2R9 ETHENYLCYCLOPROPYL}-L-PROLINAMIDE HETNAM ZN ZINC ION

HETSYN 2R9 ASUNAPREVIR

FORMUL 3 2R9 2(C35 H46 CL N5 O9 S) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *112(H2 O)

HELIX 1 1 GLU A 14 GLY A 23 1 10 HELIX 2 2 TYR A 56 GLY A 60 1 5 HELIX 3 3 ILE A 132 LYS A 136 1 5 HELIX 4 4 VAL A 172 SER A 181 1 10 HELIX 5 5 GLY B 12 GLY B 23 1 12 HELIX 6 6 TYR B 56 GLY B 60 1 5 HELIX 7 7 ILE B 132 LYS B 136 1 5 HELIX 8 8 VAL B 172 SER B 181 1 10

SHEET 1 A 7 TYR A 6 GLN A 9 0 SHEET 2 A 7 VAL A -7 ASN A -1 -1 N ASN A -1 O TYR A 6 SHEET 3 A 7 VAL A 33 SER A 37 -1 O VAL A 33 N ILE A -2 SHEET 4 A 7 THR A 42 ILE A 48 -1 O PHE A 43 N VAL A 36 SHEET 5 A 7 VAL A 51 VAL A 55 -1 O TRP A 53 N THR A 46 SHEET 6 A 7 LEU A 82 GLN A 86 -1 O TRP A 85 N LEU A 52 SHEET 7 A 7 TYR A 75 ASN A 77 -1 N ASN A 77 O LEU A 82 SHEET 1 B 7 ASP A 103 VAL A 107 0 SHEET 2 B 7 VAL A 113 ARG A 118 -1 O VAL A 116 N LEU A 104 SHEET 3 B 7 ARG A 123 PRO A 131 -1 O SER A 125 N ARG A 117 SHEET 4 B 7 VAL A 163 PRO A 171 -1 O ALA A 164 N ARG A 130 SHEET 5 B 7 ALA A 150 THR A 160 -1 N ALA A 156 O ASP A 168 SHEET 6 B 7 PRO A 142 LEU A 144 -1 N LEU A 143 O VAL A 151 SHEET 7 B 7 ASP A 103 VAL A 107 -1 N TYR A 105 O LEU A 144 SHEET 1 C 7 TYR B 6 GLN B 9 0 SHEET 2 C 7 VAL B -7 ASN B -1 -1 N ASN B -1 O TYR B 6 SHEET 3 C 7 VAL B 33 SER B 37 -1 O ILE B 35 N VAL B -5 SHEET 4 C 7 THR B 42 ILE B 48 -1 O ALA B 45 N GLN B 34 SHEET 5 C 7 VAL B 51 VAL B 55 -1 O TRP B 53 N THR B 46 SHEET 6 C 7 LEU B 82 GLN B 86 -1 O VAL B 83 N THR B 54 SHEET 7 C 7 TYR B 75 ASN B 77 -1 N ASN B 77 O LEU B 82 SHEET 1 D 7 ASP B 103 VAL B 107 0 SHEET 2 D 7 VAL B 113 ARG B 118 -1 O VAL B 116 N LEU B 104 SHEET 3 D 7 ARG B 123 PRO B 131 -1 O SER B 125 N ARG B 117 SHEET 4 D 7 VAL B 163 PRO B 171 -1 O ALA B 164 N ARG B 130 SHEET 5 D 7 ALA B 150 THR B 160 -1 N ALA B 156 O ASP B 168 SHEET 6 D 7 PRO B 142 LEU B 144 -1 N LEU B 143 O VAL B 151 SHEET 7 D 7 ASP B 103 VAL B 107 -1 N TYR B 105 O LEU B 144

LINK SG CYS A 99 ZN ZN A 302 1555 1555 2.28 LINK SG CYS A 97 ZN ZN A 302 1555 1555 2.29 LINK ND1 HIS B 149 ZN ZN B 302 1555 1555 2.32 LINK SG CYS B 97 ZN ZN B 302 1555 1555 2.35 LINK ND1 HIS A 149 ZN ZN A 302 1555 1555 2.37 LINK SG CYS A 145 ZN ZN A 302 1555 1555 2.37 LINK SG CYS B 145 ZN ZN B 302 1555 1555 2.39 LINK SG CYS B 99 ZN ZN B 302 1555 1555 2.43

SITE 1 AC1 21 PHE A 43 HIS A 57 VAL A 78 ASP A 81 SITE 2 AC1 21 LEU A 135 LYS A 136 GLY A 137 SER A 139 SITE 3 AC1 21 PHE A 154 ARG A 155 ALA A 156 ALA A 157 SITE 4 AC1 21 VAL A 158 CYS A 159 ASP A 168 HOH A 410 SITE 5 AC1 21 HOH A 436 HOH A 446 TYR B 6 ALA B 7 SITE 6 AC1 21 GLN B 8 SITE 1 AC2 4 CYS A 97 CYS A 99 CYS A 145 HIS A 149 SITE 1 AC3 21 ARG A -3 TYR A 6 ALA A 7 GLN A 8 SITE 2 AC3 21 PHE B 43 TYR B 56 HIS B 57 GLY B 58 SITE 3 AC3 21 VAL B 78 ASP B 79 ASP B 81 LEU B 135 SITE 4 AC3 21 LYS B 136 GLY B 137 SER B 139 PHE B 154 SITE 5 AC3 21 ARG B 155 ALA B 156 ALA B 157 CYS B 159 SITE 6 AC3 21 ASP B 168 SITE 1 AC4 4 CYS B 97 CYS B 99 CYS B 145 HIS B 149

CRYST1 45.412 67.761 61.307 90.00 108.46 90.00 P 1 21 1 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 0.022021 0.000000 0.007351 0.00000

SCALE2 0.000000 0.014758 0.000000 0.00000

SCALE3 0.000000 0.000000 0.017196 0.00000