HEADER TRANSFERASE 16-DEC-03 1RW8 TITLE CRYSTAL STRUCTURE OF TGF-BETA RECEPTOR I KINASE WITH ATP SITE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TGF-BETA RECEPTOR TYPE I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRUNCATED KINASE DOMAIN (RESIDUES 200-500); COMPND 5 SYNONYM: TGFR-1, TGF-BETA TYPE I RECEPTOR, SERINE/THREONINE-PROTEIN COMPND 6 KINASE RECEPTOR R4, SKR4, ACTIVIN RECEPTOR-LIKE KINASE 5, ALK-5; COMPND 7 EC: 2.7.1.37; COMPND 8 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: TRU; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS TGF-BETA RECEPTOR I, PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ZHANG,J.S.SAWYER REVDAT 3 23-AUG-23 1RW8 1 REMARK REVDAT 2 24-FEB-09 1RW8 1 VERSN REVDAT 1 01-FEB-05 1RW8 0 JRNL AUTH J.S.SAWYER,D.W.BEIGHT,K.S.BRITT,B.D.ANDERSON,R.M.CAMPBELL, JRNL AUTH 2 T.GOODSON JR.,D.K.HERRON,H.Y.LI,W.T.MCMILLEN,N.MORT, JRNL AUTH 3 S.PARSONS,E.C.SMITH,J.R.WAGNER,L.YAN,F.ZHANG,J.M.YINGLING JRNL TITL SYNTHESIS AND ACTIVITY OF NEW ARYL- AND JRNL TITL 2 HETEROARYL-SUBSTITUTED 5,6-DIHYDRO-4H-PYRROLO[1,2-B]PYRAZOLE JRNL TITL 3 INHIBITORS OF THE TRANSFORMING GROWTH FACTOR-BETA TYPE I JRNL TITL 4 RECEPTOR KINASE DOMAIN. JRNL REF BIOORG.MED.CHEM.LETT. V. 14 3581 2004 JRNL REFN ISSN 0960-894X JRNL PMID 15177479 JRNL DOI 10.1016/J.BMCL.2004.04.007 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 11890 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHTOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 607 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2418 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.58000 REMARK 3 B22 (A**2) : 0.08400 REMARK 3 B33 (A**2) : -3.67000 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) : 0.04 REMARK 3 ESD FROM SIGMAA (A) : 0.22 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) : 0.04 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.550 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.550 ; 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : 580.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE REMARK 4 REMARK 4 1RW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11890 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PY5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, ATP, MGCL2, DTT, HEXANEDIOL, PEG REMARK 280 4000, LISO4, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 -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 20.98050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.04250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.48050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.04250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.98050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.48050 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 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 LYS A 213 -99.08 -86.35 REMARK 500 GLU A 238 35.67 -87.09 REMARK 500 GLN A 250 -64.55 -103.95 REMARK 500 THR A 251 -1.50 -51.04 REMARK 500 LEU A 254 31.72 -85.64 REMARK 500 LYS A 268 83.56 -59.56 REMARK 500 THR A 274 -87.81 -37.35 REMARK 500 GLN A 275 115.14 99.01 REMARK 500 THR A 323 -90.71 -49.07 REMARK 500 GLN A 324 57.09 -94.23 REMARK 500 ARG A 332 4.14 80.12 REMARK 500 ASP A 333 43.87 -159.78 REMARK 500 ASP A 351 78.57 52.01 REMARK 500 ARG A 372 127.66 175.40 REMARK 500 VAL A 373 -151.65 -83.25 REMARK 500 MET A 390 21.04 -70.51 REMARK 500 TRP A 458 7.14 -63.05 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 580 A 501 DBREF 1RW8 A 200 500 UNP P36897 TGFR1_HUMAN 200 500 SEQRES 1 A 301 THR ILE ALA ARG THR ILE VAL LEU GLN GLU SER ILE GLY SEQRES 2 A 301 LYS GLY ARG PHE GLY GLU VAL TRP ARG GLY LYS TRP ARG SEQRES 3 A 301 GLY GLU GLU VAL ALA VAL LYS ILE PHE SER SER ARG GLU SEQRES 4 A 301 GLU ARG SER TRP PHE ARG GLU ALA GLU ILE TYR GLN THR SEQRES 5 A 301 VAL MET LEU ARG HIS GLU ASN ILE LEU GLY PHE ILE ALA SEQRES 6 A 301 ALA ASP ASN LYS ASP ASN GLY THR TRP THR GLN LEU TRP SEQRES 7 A 301 LEU VAL SER ASP TYR HIS GLU HIS GLY SER LEU PHE ASP SEQRES 8 A 301 TYR LEU ASN ARG TYR THR VAL THR VAL GLU GLY MET ILE SEQRES 9 A 301 LYS LEU ALA LEU SER THR ALA SER GLY LEU ALA HIS LEU SEQRES 10 A 301 HIS MET GLU ILE VAL GLY THR GLN GLY LYS PRO ALA ILE SEQRES 11 A 301 ALA HIS ARG ASP LEU LYS SER LYS ASN ILE LEU VAL LYS SEQRES 12 A 301 LYS ASN GLY THR CYS CYS ILE ALA ASP LEU GLY LEU ALA SEQRES 13 A 301 VAL ARG HIS ASP SER ALA THR ASP THR ILE ASP ILE ALA SEQRES 14 A 301 PRO ASN HIS ARG VAL GLY THR LYS ARG TYR MET ALA PRO SEQRES 15 A 301 GLU VAL LEU ASP ASP SER ILE ASN MET LYS HIS PHE GLU SEQRES 16 A 301 SER PHE LYS ARG ALA ASP ILE TYR ALA MET GLY LEU VAL SEQRES 17 A 301 PHE TRP GLU ILE ALA ARG ARG CYS SER ILE GLY GLY ILE SEQRES 18 A 301 HIS GLU ASP TYR GLN LEU PRO TYR TYR ASP LEU VAL PRO SEQRES 19 A 301 SER ASP PRO SER VAL GLU GLU MET ARG LYS VAL VAL CYS SEQRES 20 A 301 GLU GLN LYS LEU ARG PRO ASN ILE PRO ASN ARG TRP GLN SEQRES 21 A 301 SER CYS GLU ALA LEU ARG VAL MET ALA LYS ILE MET ARG SEQRES 22 A 301 GLU CYS TRP TYR ALA ASN GLY ALA ALA ARG LEU THR ALA SEQRES 23 A 301 LEU ARG ILE LYS LYS THR LEU SER GLN LEU SER GLN GLN SEQRES 24 A 301 GLU GLY HET 580 A 501 22 HETNAM 580 3-(4-FLUOROPHENYL)-2-(6-METHYLPYRIDIN-2-YL)-5,6- HETNAM 2 580 DIHYDRO-4H-PYRROLO[1,2-B]PYRAZOLE FORMUL 2 580 C18 H16 F N3 FORMUL 3 HOH *105(H2 O) HELIX 1 1 ILE A 201 ILE A 205 5 5 HELIX 2 2 GLU A 238 THR A 251 1 14 HELIX 3 3 SER A 287 TYR A 295 1 9 HELIX 4 4 THR A 298 MET A 318 1 21 HELIX 5 5 THR A 375 MET A 379 5 5 HELIX 6 6 ALA A 380 ASP A 385 1 6 HELIX 7 7 HIS A 392 ARG A 414 1 23 HELIX 8 8 SER A 437 CYS A 446 1 10 HELIX 9 9 PRO A 455 SER A 460 5 6 HELIX 10 10 CYS A 461 GLU A 473 1 13 HELIX 11 11 ASN A 478 ARG A 482 5 5 HELIX 12 12 THR A 484 GLY A 500 1 17 SHEET 1 A 5 VAL A 206 SER A 210 0 SHEET 2 A 5 GLU A 218 TRP A 224 -1 O ARG A 221 N GLU A 209 SHEET 3 A 5 GLU A 227 PHE A 234 -1 O VAL A 229 N GLY A 222 SHEET 4 A 5 LEU A 276 ASP A 281 -1 O LEU A 276 N PHE A 234 SHEET 5 A 5 PHE A 262 ASP A 266 -1 N ALA A 264 O VAL A 279 SHEET 1 B 3 ALA A 328 ALA A 330 0 SHEET 2 B 3 VAL A 356 ASP A 359 -1 O HIS A 358 N ALA A 328 SHEET 3 B 3 THR A 364 ASP A 366 -1 O THR A 364 N ASP A 359 SHEET 1 C 2 ILE A 339 VAL A 341 0 SHEET 2 C 2 CYS A 347 ILE A 349 -1 O CYS A 348 N LEU A 340 SITE 1 AC1 15 HOH A 20 ILE A 211 VAL A 219 ALA A 230 SITE 2 AC1 15 LYS A 232 TYR A 249 LEU A 260 LEU A 278 SITE 3 AC1 15 SER A 280 ASP A 281 TYR A 282 HIS A 283 SITE 4 AC1 15 LYS A 337 ASN A 338 LEU A 340 CRYST1 41.961 84.961 84.085 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 0.023832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011893 0.00000