1CU7 - Header Asymmetric Unit

HEADER HYDROLASE 20-AUG-99 1CU7

TITLE BOVINE TRYPSIN COMPLEXED WITH 2-[3-AMINO(IMINOMETHYL) TITLE 2 PHENOXY]-6-[3-(AMINOMETHYL)PHENOXY]-3,5-DIFLUORO-4- TITLE 3 METHYLPYRIDINE (ZK-806299), BINDING MODEL FROM DOUBLE TITLE 4 REDOR NMR AND MD SIMULATIONS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (TRYPSIN); COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.4

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGAN: PANCREAS; SOURCE 5 OTHER_DETAILS: OBTAINED FROM WORTHINGTON BIOCHEMICAL CORP.

KEYWDS HYDROLASE, SERINE PROTEINASE, REDOR, NMR, MOLECULAR KEYWDS 2 DYNAMICS, PROTEIN INHIBITOR COMPLEX

EXPDTA THEORETICAL MODEL

AUTHOR M.A.MCCARRICK,L.M.MCDOWELL,D.R.STUDELSKA,J.SCHAEFER

REVDAT 3 26-SEP-01 1CU7 3 ATOM REVDAT 2 10-APR-00 1CU7 1 JRNL REVDAT 1 03-AUG-99 1CU7 0

JRNL AUTH L.M.MCDOWELL,M.A.MCCARRICK,D.R.STUDELSKA, JRNL AUTH 2 W.J.GUILFORD,D.ARNAIZ,J.L.DALLAS,D.R.LIGHT, JRNL AUTH 3 M.WHITLOW,J.SCHAEFER JRNL TITL CONFORMATIONS OF TRYPSIN-BOUND AMIDINE INHIBITORS JRNL TITL 2 OF BLOOD COAGULANT FACTOR XA BY DOUBLE REDOR NMR JRNL TITL 3 AND MD SIMULATIONS. JRNL REF J.MED.CHEM. V. 42 3910 1999 JRNL REFN ASTM JMCMAR US ISSN 0022-2623

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.WHITLOW,D.ARNAIZ,B.O.BUCKMAN,D.D.DAVEY,B.GRIEDEL, REMARK 1 AUTH 2 W.J.GUILFORD,S.K.KOOVAKKAT,A.LIANG,R.MOHAN, REMARK 1 AUTH 3 G.B.PHILLIPS,M.SETO,K.J.SHAW,W.XU,Z.ZHAO,W.Z.XU, REMARK 1 AUTH 4 D.R.LIGHT,M.M.MORRISSEY REMARK 1 TITL CRYSTALLOGRAPHIC ANALYSIS OF POTENT AND SELECTIVE REMARK 1 TITL 2 FACTOR XA INHIBITORS COMPLEXED TO BOVINE TRYPSIN REMARK 1 REF ACTA CRYSTALLOGR., SECT.D V. 55 1395 1999 REMARK 1 REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.M.GOETZ,J.SCHAEFER REMARK 1 TITL REDOR DEPHASING BY MULTIPLE SPINS IN THE PRESENCE REMARK 1 TITL 2 OF MOLECULAR MOTION REMARK 1 REF J.MAGN.RESON. V. 127 147 1997 REMARK 1 REFN ASTM JOMRA4 US ISSN 0022-2364 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.D.BEUSEN,L.M.MCDOWELL,U.SLOMCZYNSKA,J.SCHAEFER REMARK 1 TITL SOLID-STATE NUCLEAR MAGNETIC RESONANCE ANALYSIS OF REMARK 1 TITL 2 THE CONFORMATION OF AN INHIBITOR BOUND TO REMARK 1 TITL 3 THERMOLYSIN REMARK 1 REF J.MED.CHEM. V. 38 2742 1995 REMARK 1 REFN ASTM JMCMAR US ISSN 0022-2623

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS CONSIDERED COMPLETE REMARK 3 WHEN THE THEORETICAL REDOR CURVE PREDICTED BY THE MODEL REMARK 3 MATCHED THE EXPERIMENTAL DATA. THEORETICAL REDOR CURVE REMARK 3 CALCULATIONS INCLUDED A POWDER AVERAGE OVER ALL POSSIBLE REMARK 3 ORIENTATIONS OF THE I- S INTERNUCLEAR VECTORS (SEE EQ. 22 OF REMARK 3 REF 2 AND BIOCHEMISTRY (1996) V. 35, PP. 5395-5403). FOR EACH REMARK 3 CURVE, 3 SPINS WERE INCLUDED: AN OBSERVED CARBON-13 AND TWO REMARK 3 FLUORINE-19 DEPHASING SPINS. ALL 3 SPINS WERE ASSUMED TO BE REMARK 3 100 PERCENT INCORPORATED. THE PASCAL PROGRAM USED TO COMPUTE REMARK 3 THE REDOR CURVES WAS WRITTEN BY C.A.KLUG. A THEORETICAL REDOR REMARK 3 CURVE WAS CALCULATED FOR THE MD MODEL COORDINATES, AND THE REMARK 3 RESULTS WERE USED TO ADJUST THE C-F DISTANCE RESTRAINTS FOR REMARK 3 THE NEXT MD CALCULATION. THREE ITERATIONS OF THIS TECHNIQUE REMARK 3 LEAD TO AGREEMENT BETWEEN THE THEORETICAL REDOR CURVES AND THE REMARK 3 EXPERIMENTAL POINTS. MOLECULAR DYNAMICS CALCULATIONS WERE REMARK 3 PERFORMED USING THE SANDER PROGRAM FROM THE AMBER 4.1 PACKAGE, REMARK 3 WITH HARMONIC RESTRAINTS ON NMR DETERMINED C-F DISTANCES. THE REMARK 3 FORCE CONSTANTS ON THESE RESTRAINTS WERE GRADUALLY INCREASED REMARK 3 FROM 0 KCAL/MOL TO 100 KCAL/MOL DURING THE COURSE OF THE 50 REMARK 3 PICOSECOND DYNAMIC SIMULATIONS. DISTANCE RESTRAINTS FROM FINAL REMARK 3 ITERATION: C21 - F28: 7.7 ANGSTROMS, C23 - F26: 7.4 ANGSTROMS

REMARK 4 REMARK 4 1CU7 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 7 REMARK 7 DESCRIPTION OF STRUCTURE DETERMINATION: REMARK 7 DOUBLE REDOR NMR WAS USED TO DEFINE THE CONFORMATION OF REMARK 7 THE INHIBITOR AS BOUND TO TRYPSIN. THE INHIBITOR CONTAINS REMARK 7 TWO CARBON-13 LABELS, ATOMS C23 AND C21. THE ATTACHED REMARK 7 NITROGENS (N22, N24, AND N25) ARE NITROGEN-15 LABELED IN REMARK 7 THE EXPERIMENT. NATURAL ABUNDANCE FLUORINE-19 IS THE THIRD REMARK 7 LABEL. THE REDOR EXPERIMENTS MEASURED THE 13C - 19F REMARK 7 DISTANCES, USING 13C - 15N DEPHASING TO REMOVE THE EFFECT REMARK 7 OF NATURAL ABUNDANCE 13C. SEE THE JOURNAL REFERENCE FOR A REMARK 7 MORE COMPLETE EXPERIMENTAL DESCRIPTION.

REMARK 8 REMARK 8 THE COORDINATES OF TRYPSIN WERE OBTAINED FROM THE CRYSTAL REMARK 8 STRUCTURE IN REFERENCE 1 (PDB ID 1QB6). HYDROGENS, REMARK 8 COUNTERIONS, AND A CAP OF 427 WATER MOLECULES HAVE BEEN REMARK 8 ADDED FOR THE MOLECULAR DYNAMICS CALCULATIONS USING AMBER REMARK 8 4.1 FROM UCSF. RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED REMARK 8 ON THE INHIBITOR, WATER CAP, AND PROTEIN RESIDUES REMARK 8 WITHIN 8 ANGSTROMS OF THE INHIBITOR, WITH THE PROXIMAL REMARK 8 13C - 19F DISTANCES CONSTRAINED BASED ON REMARK 8 THE REDOR EXPERIMENT. THE INITIAL BOUND CONFORMATION OF THE REMARK 8 INHIBITOR WAS TAKEN FROM THE CRYSTAL COORDINATES OF REMARK 8 REFERENCE 1. THE STRUCTURE HAS BEEN MINIMIZED FOR 3000 REMARK 8 CYCLES AFTER MD.

REMARK 9 REMARK 9 RESIDUES GLY 8 AND GLY 179 WERE NOT PART OF THE REMARK 9 THE MOLECULAR DYNAMICS MOVING SET, THUS THEY REMAIN REMARK 9 IN THEIR CRYSTALLOGRAPHIC POSITIONS FROM THE SOURCE REMARK 9 CRYSTAL STRUCTURE 1QB6

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-1999. REMARK 100 THE RCSB ID CODE IS RCSB009547.

REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QB6 RELATED DB: PDB REMARK 900 STARTING MODEL FOR MD REMARK 900 RELATED ID: 1CU8 RELATED DB: PDB REMARK 900 MD MODEL OF THE TRYPSIN-BOUND STRUCTURE OF 2,6- REMARK 900 BIS[3AMINO(IMINO)METHYL] PHENOXY-3,5-DIFLUORO-4- REMARK 900 METHYLPYRIDINE, ALSO REPORTED IN THE JOURNAL REFERENCE REMARK 900 RELATED ID: 1CU9 RELATED DB: PDB REMARK 900 MD/DISTANCE GEOMETRY MODEL OF THE TRYPSIN-BOUND STRUCTURE REMARK 900 OF 2,6-BIS[3-AMINO(IMINO)METHYL]PHENOXY-3,5-DIFLUORO-4- REMARK 900 METHYLPYRIDINE, ALSO REPORTED IN THE JOURNAL REFERENCE

DBREF 1CU7 A 1 223 UNP P00760 TRY1_BOVIN 1 223

SEQRES 1 A 223 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 A 223 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 223 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 223 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 223 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 A 223 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 A 223 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 A 223 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 A 223 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 A 223 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 A 223 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 A 223 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 A 223 THR SER ASN MET PHE CYS ALA GLY TYR LEU GLU GLY GLY SEQRES 14 A 223 LYS ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL SEQRES 15 A 223 CYS SER GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER SEQRES 16 A 223 GLY CYS ALA GLN LYS ASN LYS PRO GLY VAL TYR THR LYS SEQRES 17 A 223 VAL CYS ASN TYR VAL SER TRP ILE LYS GLN THR ILE ALA SEQRES 18 A 223 SER ASN

HET CL 225 1 HET CL 226 1 HET CL 227 1 HET CL 228 1 HET CL 229 1 HET CL 230 1 HET CL 231 1 HET CL 233 1 HET ZK9 224 48

HETNAM CL CHLORIDE ION HETNAM ZK9 [3-AMINOMETHYLPHENYL-OXY-]-[BENZAMIDIN-3-YLOXY]-3,5- HETNAM 2 ZK9 DIFLUORO-4-METHYL-PYRIDINE

HETSYN ZK9 ZK-806299

FORMUL 2 CL 8(CL 1-) FORMUL 10 ZK9 C20 H20 F2 N4 O2 2+ FORMUL 11 HOH *427(H2 O1)

HELIX 1 1 ALA A 38 TYR A 42 5 5 HELIX 2 2 SER A 144 TYR A 152 1 9 HELIX 3 3 TYR A 212 SER A 222 1 11

SHEET 1 A 7 TYR A 5 THR A 6 0 SHEET 2 A 7 LYS A 136 PRO A 141 -1 N CYS A 137 O TYR A 5 SHEET 3 A 7 GLN A 115 GLY A 120 -1 O CYS A 116 N ALA A 140 SHEET 4 A 7 PRO A 180 CYS A 183 -1 O PRO A 180 N SER A 119 SHEET 5 A 7 LYS A 186 TRP A 193 -1 O LYS A 186 N CYS A 183 SHEET 6 A 7 VAL A 205 LYS A 208 -1 N VAL A 205 O TRP A 193 SHEET 7 A 7 MET A 160 CYS A 162 -1 O PHE A 161 N TYR A 206 SHEET 1 B 7 GLN A 15 ASN A 19 0 SHEET 2 B 7 HIS A 23 ASN A 31 -1 N PHE A 24 O LEU A 18 SHEET 3 B 7 GLN A 15 ASN A 19 -1 N VAL A 16 O GLY A 27 SHEET 4 B 7 GLN A 47 LEU A 50 -1 O GLN A 47 N ASN A 19 SHEET 5 B 7 GLN A 63 VAL A 72 -1 O GLN A 63 N LEU A 50 SHEET 6 B 7 MET A 86 LEU A 90 -1 O LEU A 87 N ILE A 71 SHEET 7 B 7 TRP A 34 SER A 37 -1 O VAL A 35 N ILE A 88

SSBOND 1 CYS A 7 CYS A 137 SSBOND 2 CYS A 25 CYS A 41 SSBOND 3 CYS A 109 CYS A 210 SSBOND 4 CYS A 116 CYS A 183 SSBOND 5 CYS A 148 CYS A 162 SSBOND 6 CYS A 173 CYS A 197

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

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 1.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 1.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 1.000000 0.00000