HEADER TRANSFERASE/TRANSFERASE INHIBITOR 18-OCT-10 3PA3 TITLE X-RAY CRYSTAL STRUCTURE OF COMPOUND 70 BOUND TO HUMAN CHK1 KINASE TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE CHK1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-274; COMPND 5 EC: 2.7.11.1; COMPND 6 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: CHEK1, CHK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS KINASE, PHOSPHATASE, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.O.FISCHMANN REVDAT 2 21-FEB-24 3PA3 1 REMARK REVDAT 1 08-DEC-10 3PA3 0 JRNL AUTH L.ZHAO,Y.ZHANG,C.DAI,T.GUZI,D.WISWELL,W.SEGHEZZI,D.PARRY, JRNL AUTH 2 T.FISCHMANN,M.A.SIDDIQUI JRNL TITL DESIGN, SYNTHESIS AND SAR OF THIENOPYRIDINES AS POTENT CHK1 JRNL TITL 2 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 7216 2010 JRNL REFN ISSN 0960-894X JRNL PMID 21074424 JRNL DOI 10.1016/J.BMCL.2010.10.105 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 46007 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.65 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 3PA3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54578 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30600 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-CL PH 7.5, 1% V/V N REMARK 280 -BUTANOL, 2.5% V/V DMSO, 25% V/V GLYCEROL, 6-12% PEG 3.25K, 2.5 REMARK 280 MM TCEP-CL, 10 MM NA2-DITHIONITE, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.94500 REMARK 290 SMTRY3 2 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: PISA 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 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 ALA A 2 REMARK 465 VAL A 3 REMARK 465 LYS A 43 REMARK 465 ARG A 44 REMARK 465 ALA A 45 REMARK 465 VAL A 46 REMARK 465 ASP A 47 REMARK 465 CYS A 48 REMARK 465 PRO A 49 REMARK 465 GLU A 50 REMARK 465 ALA A 273 REMARK 465 LYS A 274 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 PRO A 4 N CA CB CG CD REMARK 470 MET A 42 C O CB CG SD CE REMARK 470 GLY A 272 CA C O 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 PHE A 5 -10.75 94.62 REMARK 500 ASN A 63 86.14 -151.04 REMARK 500 GLU A 76 68.06 -116.58 REMARK 500 ASP A 99 -0.02 69.53 REMARK 500 ILE A 100 -50.97 -120.58 REMARK 500 ARG A 129 -1.43 74.44 REMARK 500 ASP A 130 45.35 -149.73 REMARK 500 ASP A 148 75.54 69.42 REMARK 500 LYS A 270 145.91 -173.86 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 C70 A 1 DBREF 3PA3 A 2 274 UNP O14757 CHK1_HUMAN 2 274 SEQRES 1 A 273 ALA VAL PRO PHE VAL GLU ASP TRP ASP LEU VAL GLN THR SEQRES 2 A 273 LEU GLY GLU GLY ALA TYR GLY GLU VAL GLN LEU ALA VAL SEQRES 3 A 273 ASN ARG VAL THR GLU GLU ALA VAL ALA VAL LYS ILE VAL SEQRES 4 A 273 ASP MET LYS ARG ALA VAL ASP CYS PRO GLU ASN ILE LYS SEQRES 5 A 273 LYS GLU ILE CYS ILE ASN LYS MET LEU ASN HIS GLU ASN SEQRES 6 A 273 VAL VAL LYS PHE TYR GLY HIS ARG ARG GLU GLY ASN ILE SEQRES 7 A 273 GLN TYR LEU PHE LEU GLU TYR CYS SER GLY GLY GLU LEU SEQRES 8 A 273 PHE ASP ARG ILE GLU PRO ASP ILE GLY MET PRO GLU PRO SEQRES 9 A 273 ASP ALA GLN ARG PHE PHE HIS GLN LEU MET ALA GLY VAL SEQRES 10 A 273 VAL TYR LEU HIS GLY ILE GLY ILE THR HIS ARG ASP ILE SEQRES 11 A 273 LYS PRO GLU ASN LEU LEU LEU ASP GLU ARG ASP ASN LEU SEQRES 12 A 273 LYS ILE SER ASP PHE GLY LEU ALA THR VAL PHE ARG TYR SEQRES 13 A 273 ASN ASN ARG GLU ARG LEU LEU ASN LYS MET CYS GLY THR SEQRES 14 A 273 LEU PRO TYR VAL ALA PRO GLU LEU LEU LYS ARG ARG GLU SEQRES 15 A 273 PHE HIS ALA GLU PRO VAL ASP VAL TRP SER CYS GLY ILE SEQRES 16 A 273 VAL LEU THR ALA MET LEU ALA GLY GLU LEU PRO TRP ASP SEQRES 17 A 273 GLN PRO SER ASP SER CYS GLN GLU TYR SER ASP TRP LYS SEQRES 18 A 273 GLU LYS LYS THR TYR LEU ASN PRO TRP LYS LYS ILE ASP SEQRES 19 A 273 SER ALA PRO LEU ALA LEU LEU HIS LYS ILE LEU VAL GLU SEQRES 20 A 273 ASN PRO SER ALA ARG ILE THR ILE PRO ASP ILE LYS LYS SEQRES 21 A 273 ASP ARG TRP TYR ASN LYS PRO LEU LYS LYS GLY ALA LYS HET C70 A 1 26 HETNAM C70 2-(4-CHLOROPHENYL)-4-[(3S)-PIPERIDIN-3- HETNAM 2 C70 YLAMINO]THIENO[2,3-D]PYRIDAZINE-7-CARBOXAMIDE FORMUL 2 C70 C18 H18 CL N5 O S FORMUL 3 HOH *249(H2 O) HELIX 1 1 ASN A 51 LYS A 60 1 10 HELIX 2 2 PHE A 93 ILE A 96 5 4 HELIX 3 3 PRO A 103 ILE A 124 1 22 HELIX 4 4 LYS A 132 GLU A 134 5 3 HELIX 5 5 THR A 170 VAL A 174 5 5 HELIX 6 6 ALA A 175 ARG A 181 1 7 HELIX 7 7 HIS A 185 GLY A 204 1 20 HELIX 8 8 CYS A 215 GLU A 223 1 9 HELIX 9 9 PRO A 230 ILE A 234 5 5 HELIX 10 10 ASP A 235 LEU A 246 1 12 HELIX 11 11 THR A 255 LYS A 260 1 6 SHEET 1 A 5 TRP A 9 GLY A 16 0 SHEET 2 A 5 GLY A 21 ASN A 28 -1 O VAL A 23 N LEU A 15 SHEET 3 A 5 ALA A 34 ASP A 41 -1 O ILE A 39 N GLU A 22 SHEET 4 A 5 ILE A 79 GLU A 85 -1 O LEU A 84 N ALA A 36 SHEET 5 A 5 PHE A 70 ARG A 75 -1 N GLY A 72 O PHE A 83 SHEET 1 B 3 GLY A 90 GLU A 91 0 SHEET 2 B 3 LEU A 136 LEU A 138 -1 O LEU A 138 N GLY A 90 SHEET 3 B 3 LEU A 144 ILE A 146 -1 O LYS A 145 N LEU A 137 SHEET 1 C 2 ILE A 126 THR A 127 0 SHEET 2 C 2 THR A 153 VAL A 154 -1 O THR A 153 N THR A 127 SHEET 1 D 2 ARG A 156 TYR A 157 0 SHEET 2 D 2 ARG A 160 GLU A 161 -1 O ARG A 160 N TYR A 157 CISPEP 1 ASN A 229 PRO A 230 0 1.30 SITE 1 AC1 16 LEU A 15 GLU A 17 ALA A 36 GLU A 85 SITE 2 AC1 16 TYR A 86 CYS A 87 SER A 88 GLY A 90 SITE 3 AC1 16 GLU A 91 GLU A 134 ASN A 135 LEU A 137 SITE 4 AC1 16 ASP A 148 HOH A 440 HOH A 441 HOH A 463 CRYST1 44.910 65.890 58.180 90.00 94.26 90.00 P 1 21 1 2 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 0.022267 0.000000 0.001659 0.00000 SCALE2 0.000000 0.015177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017236 0.00000