HEADER HYDROLASE 28-MAR-03 1OWI TITLE SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 179-423; COMPND 5 SYNONYM: UPA, U-PLASMINOGEN ACTIVATOR; COMPND 6 EC: 3.4.21.73; COMPND 7 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: PLAU; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS PLASMINOGEN ACTIVATION, HYDROLASE, SERINE PROTEASE, GLYCOPROTEIN, KEYWDS 2 KRINGLE, EGF-LIKE DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.WENDT,T.W.ROCKWAY,A.GEYER,W.MCCLELLAN,M.WEITZBERG,X.ZHAO, AUTHOR 2 R.MANTEI,V.L.NIENABER,K.STEWART,V.KLINGHOFER,V.L.GIRANDA REVDAT 4 11-OCT-17 1OWI 1 REMARK REVDAT 3 24-FEB-09 1OWI 1 VERSN REVDAT 2 20-JAN-04 1OWI 1 JRNL REVDAT 1 30-SEP-03 1OWI 0 JRNL AUTH M.D.WENDT,T.W.ROCKWAY,A.GEYER,W.MCCLELLAN,M.WEITZBERG, JRNL AUTH 2 X.ZHAO,R.MANTEI,V.L.NIENABER,K.STEWART,V.KLINGHOFER, JRNL AUTH 3 V.L.GIRANDA JRNL TITL IDENTIFICATION OF NOVEL BINDING INTERACTIONS IN THE JRNL TITL 2 DEVELOPMENT OF POTENT, SELECTIVE 2-NAPHTHAMIDINE INHIBITORS JRNL TITL 3 OF UROKINASE. SYNTHESIS, STRUCTURAL ANALYSIS, AND SAR OF JRNL TITL 4 N-PHENYL AMIDE 6-SUBSTITUTION. JRNL REF J.MED.CHEM. V. 47 303 2004 JRNL REFN ISSN 0022-2623 JRNL PMID 14711304 JRNL DOI 10.1021/JM0300072 REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 63.0 REMARK 3 NUMBER OF REFLECTIONS : 3480 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 SET) : 0.286 REMARK 3 FREE R VALUE : 0.349 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 358 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.018 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 37.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 305 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 35 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.065 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1933 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 117.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 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) : 1.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.640 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM11.WAT REMARK 3 PARAMETER FILE 2 : PARVICKI.PRO REMARK 3 PARAMETER FILE 3 : PARAM19X.PRO REMARK 3 PARAMETER FILE 4 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 5 : A276426.XPRM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 160 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4691 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 REMARK 200 RESOLUTION RANGE LOW (A) : 34.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 27.58000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.58000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.50000 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 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 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 CYS A 120 SG 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 VAL A 29 -77.68 -102.32 REMARK 500 SER A 42 -147.76 -130.49 REMARK 500 LYS A 84 4.56 -68.04 REMARK 500 ARG A 103 132.71 -171.05 REMARK 500 CYS A 109 -150.69 -91.23 REMARK 500 MET A 124 135.76 -39.34 REMARK 500 ASN A 126 84.22 -151.67 REMARK 500 TYR A 171 -101.97 -114.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 426 A 245 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FV9 RELATED DB: PDB REMARK 900 RELATED ID: 1OWD RELATED DB: PDB REMARK 900 RELATED ID: 1OWE RELATED DB: PDB REMARK 900 RELATED ID: 1OWH RELATED DB: PDB REMARK 900 RELATED ID: 1OWJ RELATED DB: PDB REMARK 900 RELATED ID: 1OWK RELATED DB: PDB DBREF 1OWI A 1 244 UNP P00749 UROK_HUMAN 179 423 SEQRES 1 A 245 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 A 245 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 A 245 VAL THR TYR VAL CYS GLY GLY SER LEU MET SER PRO CYS SEQRES 4 A 245 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 A 245 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 A 245 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 A 245 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 A 245 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 A 245 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 A 245 GLN THR ILE CYS LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 A 245 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 A 245 ASN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 A 245 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 A 245 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 A 245 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 A 245 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 A 245 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 A 245 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 A 245 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR HET 426 A 245 28 HETNAM 426 6-[(Z)-AMINO(IMINO)METHYL]-N-[3-(CYCLOPENTYLOXY) HETNAM 2 426 PHENYL]-2-NAPHTHAMIDE HETSYN 426 6-[N-(3-CYCLOPENTYLOXYPHENYL)CARBAMYL]-2- HETSYN 2 426 NAPHTHALENECARBOXAMIDINE FORMUL 2 426 C23 H23 N3 O2 HELIX 1 1 THR A 8 GLN A 12 5 5 HELIX 2 2 ALA A 43 PHE A 47 5 5 HELIX 3 3 LYS A 52 GLU A 54 5 3 HELIX 4 4 SER A 162 GLN A 167 1 6 HELIX 5 5 TYR A 172 VAL A 176 5 5 HELIX 6 6 PHE A 236 HIS A 243 1 8 SHEET 1 A 8 GLU A 5 PHE A 6 0 SHEET 2 A 8 LYS A 154 ILE A 161 -1 O MET A 155 N GLU A 5 SHEET 3 A 8 SER A 133 GLY A 138 -1 N CYS A 134 O VAL A 158 SHEET 4 A 8 PRO A 200 LEU A 205 -1 O PRO A 200 N THR A 137 SHEET 5 A 8 ARG A 208 TRP A 217 -1 N ARG A 208 O LEU A 205 SHEET 6 A 8 GLY A 228 ARG A 232 -1 N VAL A 229 O TRP A 217 SHEET 7 A 8 MET A 180 ALA A 184 -1 N LEU A 181 O TYR A 230 SHEET 8 A 8 LYS A 154 ILE A 161 -1 O LYS A 159 N ALA A 184 SHEET 1 B 7 PHE A 15 ARG A 21 0 SHEET 2 B 7 VAL A 26 SER A 36 -1 O THR A 27 N ARG A 20 SHEET 3 B 7 TRP A 39 SER A 42 -1 O TRP A 39 N MET A 35 SHEET 4 B 7 ALA A 98 ARG A 103 -1 N ALA A 98 O SER A 42 SHEET 5 B 7 MET A 73 LEU A 82 -1 N GLU A 76 O ARG A 103 SHEET 6 B 7 TYR A 56 LEU A 60 -1 O TYR A 56 N VAL A 77 SHEET 7 B 7 PHE A 15 ARG A 21 -1 O ALA A 17 N TYR A 59 SHEET 1 C 2 SER A 87 ALA A 88 0 SHEET 2 C 2 HIS A 93 HIS A 94 -1 N HIS A 94 O SER A 87 SSBOND 1 CYS A 30 CYS A 46 1555 1555 2.03 SSBOND 2 CYS A 38 CYS A 109 1555 1555 2.03 SSBOND 3 CYS A 134 CYS A 203 1555 1555 2.03 SSBOND 4 CYS A 166 CYS A 182 1555 1555 2.03 SSBOND 5 CYS A 193 CYS A 221 1555 1555 2.03 SITE 1 AC1 9 HIS A 45 TYR A 86 ALA A 88 ASP A 191 SITE 2 AC1 9 SER A 192 GLN A 194 SER A 197 GLY A 220 SITE 3 AC1 9 CYS A 221 CRYST1 55.160 53.000 82.300 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 0.018129 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012151 0.00000 MASTER 253 0 1 6 17 0 3 6 0 0 0 19 END