PDB Short entry for 2VIP HEADER HYDROLASE 05-DEC-07 2VIP TITLE FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY TITLE 2 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 179-431; COMPND 5 SYNONYM: UROKINASE-TYPE PLASMINOGEN ACTIVATOR, UPA, U-PLASMINOGEN COMPND 6 ACTIVATOR; COMPND 7 EC: 3.4.21.73; COMPND 8 ENGINEERED: YES; COMPND 9 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLASMINOGEN ACTIVATION, EGF-LIKE DOMAIN, BLOOD COAGULATION, KEYWDS 2 INHIBITOR, POLYMORPHISM, GLYCOPROTEIN, FIBRINOLYSIS, KRINGLE, KEYWDS 3 ZYMOGEN, SECRETED, PROTEASE, HYDROLASE, UROKINASE-TYPE PLASMINOGEN KEYWDS 4 ACTIVATOR, PHARMACEUTICAL, SERINE PROTEASE, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR M.FREDERICKSON,O.CALLAGHAN,G.CHESSARI,M.CONGREVE,S.R.COWAN, AUTHOR 2 J.E.MATTHEWS,R.MCMENAMIN,D.SMITH,M.VINKOVIC,N.G.WALLIS REVDAT 3 05-JUL-17 2VIP 1 REMARK REVDAT 2 24-FEB-09 2VIP 1 VERSN REVDAT 1 22-JAN-08 2VIP 0 JRNL AUTH M.FREDERICKSON,O.CALLAGHAN,G.CHESSARI,M.CONGREVE,S.R.COWAN, JRNL AUTH 2 J.E.MATTHEWS,R.MCMENAMIN,D.SMITH,M.VINKOVIC,N.G.WALLIS JRNL TITL FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY JRNL TITL 2 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN JRNL TITL 3 ACTIVATOR JRNL REF J.MED.CHEM. V. 51 183 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18163548 JRNL DOI 10.1021/JM701359Z REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.1.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.4 REMARK 3 NUMBER OF REFLECTIONS : 20118 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 999 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL REMARK 3 BOND ANGLES : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2VIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034671. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.6 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC BLUE CONFOCAL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20118 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 27.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 18.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 (%): 27.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 22-24% REMARK 280 PEG4000, 0.17M (NH4)2SO4, 15% GLYCEROL, 0.1M NA(CH3COO) PH=4.0; REMARK 280 THEN SOAKED IN 0.01M COMPOUND, 28% PEG4000, 0.29M HEPES PH=6.6, REMARK 280 5% GLYCEROL, 0.001M NA(CH3COO), 0.001M (NH4)2SO4, 10% DMSO, PH REMARK 280 6.6 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 26.24400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.51450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.19100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.51450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.24400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.19100 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, MET 214 TO ILE REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 299 TO SER 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 ASN A 246 REMARK 465 GLY A 247 REMARK 465 LEU A 248 REMARK 465 ALA A 249 REMARK 465 LEU A 250 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 GLU A 245 CA C O CB CG CD OE1 REMARK 470 GLU A 245 OE2 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 2099 O HOH A 2110 1.75 REMARK 500 O HOH A 2155 O HOH A 2210 2.06 REMARK 500 O HOH A 2116 O HOH A 2296 2.07 REMARK 500 O HOH A 2018 O HOH A 2120 2.09 REMARK 500 O HOH A 2252 O HOH A 2253 2.12 REMARK 500 O HOH A 2021 O HOH A 2120 2.14 REMARK 500 O HOH A 2165 O HOH A 2358 2.16 REMARK 500 O HOH A 2311 O HOH A 2316 2.17 REMARK 500 O HOH A 2158 O HOH A 2210 2.18 REMARK 500 O HOH A 2223 O HOH A 2224 2.18 REMARK 500 O HOH A 2127 O HOH A 2311 2.18 REMARK 500 O HOH A 2277 O HOH A 2279 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 2275 O HOH A 2338 3655 1.80 REMARK 500 O HOH A 2086 O HOH A 2187 4456 2.12 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 GLN A 27 56.31 -142.89 REMARK 500 SER A 54 -155.79 -146.49 REMARK 500 TYR A 171 -109.96 -90.23 REMARK 500 SER A 214 -58.78 -126.63 REMARK 500 THR A 242 53.84 -90.82 REMARK 500 LYS A 243 -122.26 -144.51 REMARK 500 GLU A 244 -21.67 -153.04 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 A2023 DISTANCE = 8.49 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A2025 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH A2041 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2060 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A2104 DISTANCE = 5.97 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE L1R A1247 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VIV RELATED DB: PDB REMARK 900 FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY REMARK 900 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1C5X RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, REMARK 900 SUB- MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1GJ9 RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 2VIO RELATED DB: PDB REMARK 900 FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY REMARK 900 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1W0Z RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1FV9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MICROUROKINASE IN COMPLEX WITH 2-AMINO-5- REMARK 900 HYDROXY-BENZIMIDAZOLE REMARK 900 RELATED ID: 1VJA RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN-JT464 COMPLEX REMARK 900 RELATED ID: 1GJ8 RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 1W11 RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1SQO RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1GJD RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 1W10 RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1OWK RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1W12 RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1GI9 RELATED DB: PDB REMARK 900 A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED REMARK 900 SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE REMARK 900 RELATED ID: 1O5A RELATED DB: PDB REMARK 900 DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTSAT THE REMARK 900 S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190UPA) REMARK 900 RELATED ID: 1C5Z RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, REMARK 900 SUB- MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1OWJ RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1GI7 RELATED DB: PDB REMARK 900 A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED REMARK 900 SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE REMARK 900 RELATED ID: 1O5B RELATED DB: PDB REMARK 900 DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTSAT THE REMARK 900 S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190UPA) REMARK 900 RELATED ID: 1GJC RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 1SC8 RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN-J435 COMPLEX REMARK 900 RELATED ID: 1GJA RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 1O3P RELATED DB: PDB REMARK 900 ELABORATE MANIFOLD OF SHORT HYDROGEN BOND ARRAYS MEDIATINGBINDING REMARK 900 OF ACTIVE SITE- DIRECTED SERINE PROTEASE INHIBITORS REMARK 900 RELATED ID: 1OWE RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1SQA RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1GJB RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 2VIW RELATED DB: PDB REMARK 900 FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY REMARK 900 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1F92 RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B CHAIN-UKI- 1D COMPLEX REMARK 900 RELATED ID: 1OWI RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1KDU RELATED DB: PDB REMARK 900 PLASMINOGEN ACTIVATOR (UROKINASE-TYPE, KRINGLE DOMAIN) (U-PA K) REMARK 900 (NMR, MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 2VIN RELATED DB: PDB REMARK 900 FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY REMARK 900 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1SQT RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1F5L RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN- AMILORIDE COMPLEX REMARK 900 RELATED ID: 1OWD RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1EJN RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VIQ RELATED DB: PDB REMARK 900 FRAGMENT-BASED DISCOVERY OF MEXILETINE DERIVATIVES AS ORALLY REMARK 900 BIOAVAILABLE INHIBITORS OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1LMW RELATED DB: PDB REMARK 900 LMW U-PA STRUCTURE COMPLEXED WITH EGRCMK ( GLU-GLY-ARG CHLOROMETHYL REMARK 900 KETONE) REMARK 900 RELATED ID: 1U6Q RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMADINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1GI8 RELATED DB: PDB REMARK 900 A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED REMARK 900 SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE REMARK 900 RELATED ID: 2JDE RELATED DB: PDB REMARK 900 UROKINASE-TYPE PLASMINOGEN ACTIVATOR INHIBITOR COMPLEX WITHA 1-(7- REMARK 900 SULPHOAMIDOISOQUINOLINYL) GUANIDINE REMARK 900 RELATED ID: 1C5Y RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, REMARK 900 SUB- MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1W14 RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1VJ9 RELATED DB: PDB REMARK 900 UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN-JT464 COMPLEX REMARK 900 RELATED ID: 1W13 RELATED DB: PDB REMARK 900 UPA REMARK 900 RELATED ID: 1GJ7 RELATED DB: PDB REMARK 900 ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OFSER190 REMARK 900 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS REMARK 900 RELATED ID: 1C5W RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, REMARK 900 SUB- MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1OWH RELATED DB: PDB REMARK 900 SUBSTITUTED 2-NAPHTHAMIDINE INHIBITORS OF UROKINASE REMARK 900 RELATED ID: 1O5C RELATED DB: PDB REMARK 900 DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTSAT THE REMARK 900 S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190UPA) DBREF 2VIP A 16 250 UNP P00749 UROK_HUMAN 179 431 SEQADV 2VIP ILE A 47 UNP P00749 MET 214 ENGINEERED MUTATION SEQADV 2VIP SER A 122 UNP P00749 CYS 299 ENGINEERED MUTATION SEQRES 1 A 253 ILE ILE GLY GLY GLU PHE THR THR ILE GLU ASN GLN PRO SEQRES 2 A 253 TRP PHE ALA ALA ILE TYR ARG ARG HIS ARG GLY GLY SER SEQRES 3 A 253 VAL THR TYR VAL CYS GLY GLY SER LEU ILE SER PRO CYS SEQRES 4 A 253 TRP VAL ILE SER ALA THR HIS CYS PHE ILE ASP TYR PRO SEQRES 5 A 253 LYS LYS GLU ASP TYR ILE VAL TYR LEU GLY ARG SER ARG SEQRES 6 A 253 LEU ASN SER ASN THR GLN GLY GLU MET LYS PHE GLU VAL SEQRES 7 A 253 GLU ASN LEU ILE LEU HIS LYS ASP TYR SER ALA ASP THR SEQRES 8 A 253 LEU ALA HIS HIS ASN ASP ILE ALA LEU LEU LYS ILE ARG SEQRES 9 A 253 SER LYS GLU GLY ARG CYS ALA GLN PRO SER ARG THR ILE SEQRES 10 A 253 GLN THR ILE SER LEU PRO SER MET TYR ASN ASP PRO GLN SEQRES 11 A 253 PHE GLY THR SER CYS GLU ILE THR GLY PHE GLY LYS GLU SEQRES 12 A 253 ASN SER THR ASP TYR LEU TYR PRO GLU GLN LEU LYS MET SEQRES 13 A 253 THR VAL VAL LYS LEU ILE SER HIS ARG GLU CYS GLN GLN SEQRES 14 A 253 PRO HIS TYR TYR GLY SER GLU VAL THR THR LYS MET LEU SEQRES 15 A 253 CYS ALA ALA ASP PRO GLN TRP LYS THR ASP SER CYS GLN SEQRES 16 A 253 GLY ASP SER GLY GLY PRO LEU VAL CYS SER LEU GLN GLY SEQRES 17 A 253 ARG MET THR LEU THR GLY ILE VAL SER TRP GLY ARG GLY SEQRES 18 A 253 CYS ALA LEU LYS ASP LYS PRO GLY VAL TYR THR ARG VAL SEQRES 19 A 253 SER HIS PHE LEU PRO TRP ILE ARG SER HIS THR LYS GLU SEQRES 20 A 253 GLU ASN GLY LEU ALA LEU HET ACT A1245 4 HET SO4 A1246 5 HET L1R A1247 50 HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETNAM L1R 4-(2-AMINOETHOXY)-3,5-DICHLORO-N-[3-(1-METHYLETHOXY) HETNAM 2 L1R PHENYL]BENZAMIDE FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 SO4 O4 S 2- FORMUL 4 L1R C18 H20 CL2 N2 O3 FORMUL 5 HOH *387(H2 O) HELIX 1 1 THR A 23 GLN A 27 5 5 HELIX 2 2 ALA A 55 PHE A 59 5 5 HELIX 3 3 LYS A 61 GLU A 62A 5 3 HELIX 4 4 SER A 164 GLN A 169 1 6 HELIX 5 5 TYR A 172 VAL A 176 5 5 HELIX 6 6 PHE A 234 THR A 242 1 9 SHEET 1 AA 9 GLU A 20 PHE A 21 0 SHEET 2 AA 9 LYS A 156 ILE A 163 -1 O MET A 157 N GLU A 20 SHEET 3 AA 9 MET A 180 ALA A 184 -1 O CYS A 182 N ILE A 163 SHEET 4 AA 9 GLY A 226 ARG A 230 -1 O GLY A 226 N ALA A 183 SHEET 5 AA 9 ARG A 206 TRP A 215 -1 O ILE A 212 N THR A 229 SHEET 6 AA 9 PRO A 198 LEU A 203 -1 O LEU A 199 N GLY A 211 SHEET 7 AA 9 SER A 135 GLY A 140 -1 O GLU A 137 N VAL A 200 SHEET 8 AA 9 LYS A 156 ILE A 163 1 O LYS A 156 N GLY A 140 SHEET 9 AA 9 GLU A 20 PHE A 21 -1 O GLU A 20 N MET A 157 SHEET 1 AB 8 PHE A 30 ARG A 36 0 SHEET 2 AB 8 VAL A 38 SER A 48 -1 O THR A 39 N ARG A 35 SHEET 3 AB 8 TRP A 51 SER A 54 -1 O TRP A 51 N ILE A 47 SHEET 4 AB 8 ALA A 104 ARG A 109 -1 O ALA A 104 N SER A 54 SHEET 5 AB 8 MET A 81 LEU A 90 -1 O GLU A 84 N ARG A 109 SHEET 6 AB 8 TYR A 64 LEU A 68 -1 O TYR A 64 N VAL A 85 SHEET 7 AB 8 PHE A 30 ARG A 36 -1 O ALA A 32 N TYR A 67 SHEET 8 AB 8 PHE A 30 ARG A 36 0 SHEET 1 AC 2 SER A 95 ALA A 96 0 SHEET 2 AC 2 HIS A 99 HIS A 100 -1 O HIS A 100 N SER A 95 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.02 SSBOND 2 CYS A 50 CYS A 111 1555 1555 2.03 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.02 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.03 SITE 1 AC1 5 HIS A 57 TYR A 151 GLY A 193 SER A 195 SITE 2 AC1 5 L1R A1247 SITE 1 AC2 8 LYS A 61 HIS A 100 THR A 177 LYS A 179 SITE 2 AC2 8 MET A 180 HOH A2384 HOH A2385 HOH A2386 SITE 1 AC3 20 HIS A 57 CYS A 58 ILE A 60 TYR A 94 SITE 2 AC3 20 HIS A 99 ASP A 189 SER A 190 CYS A 191 SITE 3 AC3 20 GLN A 192 SER A 195 VAL A 213 SER A 214 SITE 4 AC3 20 TRP A 215 GLY A 216 GLY A 219 CYS A 220 SITE 5 AC3 20 ACT A1245 HOH A2059 HOH A2191 HOH A2387 CRYST1 52.488 54.382 81.029 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 0.019052 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012341 0.00000