HEADER HYDROLASE 14-DEC-05 2FDZ OBSLTE 24-APR-07 2FDZ 1VSN TITLE CRYSTAL STRUCTURE OF A POTENT SMALL MOLECULE INHIBITOR TITLE 2 BOUND TO CATHEPSIN K COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATHEPSIN K; COMPND 5 SYNONYM: CATHEPSIN O, CATHEPSIN X, CATHEPSIN O2; COMPND 6 EC: 3.4.22.38; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: CTSK, CTSO, CTSO2; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: YEAST; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GS 115 KEYWDS OSTEOPOROSIS, STRUCTURE-GUIDED DRUG DESIGN, PROTEAE EXPDTA X-RAY DIFFRACTION AUTHOR M.MCGRATH REVDAT 2 24-APR-07 2FDZ 1 OBSLTE REVDAT 1 28-NOV-06 2FDZ 0 JRNL AUTH C.S.LI,D.DESCHENES,S.DESMARAIS,J.P.FALGUEYRET, JRNL AUTH 2 J.Y.GAUTHIER,D.B.KIMMEL,M.E.MCGRATH,D.J.MCKAY, JRNL AUTH 3 M.D.PERCIVAL,D.RIENDEAU,S.B.RODAN,V.L.TRUONG, JRNL AUTH 4 G.WESOLOWSKI,R.ZAMBONI,W.C.BLACK JRNL TITL IDENTIFICATION OF A POTENT AND SELECTIVE NON-BASIC JRNL TITL 2 CATHEPSIN K INHIBITOR. JRNL REF BIOORG.MED.CHEM.LETT. V. 16 1985 2006 JRNL REFN ASTM BMCLE8 UK ISSN 0960-894X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 13292 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1333 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 (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 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 : 1615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.47 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 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.680 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FDZ COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-2005. REMARK 100 THE RCSB ID CODE IS RCSB035762. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-2002 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.60 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : DTREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16006 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 30.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 71.6 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) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 10.9 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: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MG FORMATE, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 19.21000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.21000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.50000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 46 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 LEU A 162 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LYS A 193 CA - CB - CG ANGL. DEV. = 13.8 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ALA A 146 149.94 63.54 DBREF 2FDZ A 1 211 UNP P43235 CATK_HUMAN 115 329 SEQADV 2FDZ ILE A 5 UNP P43235 VAL 119 CONFLICT SEQADV 2FDZ ALA A 41 UNP P43235 LYS 155 CONFLICT SEQADV 2FDZ ALA A 44 UNP P43235 LYS 158 CONFLICT SEQADV 2FDZ ALA A 49 UNP P43235 SER 163 CONFLICT SEQADV 2FDZ ARG A 77 UNP P43235 LYS 191 CONFLICT SEQADV 2FDZ ASP A 92 UNP P43235 GLU 207 CONFLICT SEQADV 2FDZ ALA A 119 UNP P43235 LYS 233 CONFLICT SEQADV 2FDZ ALA A 127 UNP P43235 ARG 241 CONFLICT SEQADV 2FDZ ALA A 146 UNP P43235 LYS 261 CONFLICT SEQADV 2FDZ ASN A 152 UNP P43235 SER 268 CONFLICT SEQADV 2FDZ SER A 154 UNP P43235 ASN 270 CONFLICT SEQADV 2FDZ ALA A 1156 UNP P43235 ASN 273 CONFLICT SEQADV 2FDZ ALA A 2168 UNP P43235 LYS 287 CONFLICT SEQADV 2FDZ SER A 180 UNP P43235 ASN 301 CONFLICT SEQADV 2FDZ ALA A 184 UNP P43235 LYS 305 CONFLICT SEQRES 1 A 215 ALA PRO ASP SER ILE ASP TYR ARG LYS LYS GLY TYR VAL SEQRES 2 A 215 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER SER VAL GLY ALA LEU GLU GLY GLN LEU LYS SEQRES 4 A 215 LYS ALA THR GLY ALA LEU LEU ASN LEU ALA PRO GLN ASN SEQRES 5 A 215 LEU VAL ASP CYS VAL SER GLU ASN ASP GLY CYS GLY GLY SEQRES 6 A 215 GLY TYR MET THR ASN ALA PHE GLN TYR VAL GLN ARG ASN SEQRES 7 A 215 ARG GLY ILE ASP SER GLU ASP ALA TYR PRO TYR VAL GLY SEQRES 8 A 215 GLN ASP GLU SER CYS MET TYR ASN PRO THR GLY LYS ALA SEQRES 9 A 215 ALA LYS CYS ARG GLY TYR ARG GLU ILE PRO GLU GLY ASN SEQRES 10 A 215 GLU ALA ALA LEU LYS ARG ALA VAL ALA ALA VAL GLY PRO SEQRES 11 A 215 VAL SER VAL ALA ILE ASP ALA SER LEU THR SER PHE GLN SEQRES 12 A 215 PHE TYR SER ALA GLY VAL TYR TYR ASP GLU ASN CYS SER SEQRES 13 A 215 SER ASP ALA LEU ASN HIS ALA VAL LEU ALA VAL GLY TYR SEQRES 14 A 215 GLY ILE GLN ALA GLY ASN LYS HIS TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP GLY GLU SER TRP GLY ASN ALA GLY TYR ILE LEU SEQRES 16 A 215 MET ALA ARG ASN LYS ASN ASN ALA CYS GLY ILE ALA ASN SEQRES 17 A 215 LEU ALA SER PHE PRO LYS MET HELIX 1 1 SER A 24 GLY A 43 1 20 HELIX 2 2 ALA A 49 VAL A 57 1 9 HELIX 3 3 ASP A 61 GLY A 65 5 5 HELIX 4 4 TYR A 67 ARG A 1078 1 13 HELIX 5 5 ASN A 98 THR A 100 5 3 HELIX 6 6 ASN A 117 GLY A 128 1 13 HELIX 7 7 LEU A 138 PHE A 143 1 6 HELIX 8 8 ASN A 198 ILE A 202 5 5 SHEET 1 A 3 ILE A 5 ASP A 6 0 SHEET 2 A 3 HIS A 159 GLN A1168 -1 O TYR A 166 N ILE A 5 SHEET 3 A 3 VAL A 130 ILE A 134 -1 N VAL A 132 O VAL A 161 SHEET 1 B 5 ILE A 5 ASP A 6 0 SHEET 2 B 5 HIS A 159 GLN A1168 -1 O TYR A 166 N ILE A 5 SHEET 3 B 5 ASN A4168 LYS A 174 -1 O LYS A 174 N LEU A 162 SHEET 4 B 5 TYR A 186 ALA A 190 -1 O ILE A 187 N ILE A 173 SHEET 5 B 5 VAL A 148 TYR A 149 1 N TYR A 149 O LEU A 188 SHEET 1 C 2 ILE A 80 ASP A 81 0 SHEET 2 C 2 LYS A 102 ALA A 105 -1 O ALA A 103 N ILE A 80 SHEET 1 D 2 TYR A 110 GLU A 112 0 SHEET 2 D 2 SER A 207 PRO A 209 -1 O PHE A 208 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 SSBOND 2 CYS A 56 CYS A 95 SSBOND 3 CYS A 153 CYS A 200 CRYST1 38.420 51.000 104.200 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 0.026028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009597 0.00000