HEADER TRANSFERASE/TRANSFERASE INHIBITOR 19-OCT-11 3U9N TITLE X-RAY CRYSTAL STRUCTURE OF COMPOUND 1 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: KINASE DOMAIN, UPN 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_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS PROTEIN KINASE DOMAIN, ATPASE, ATP BINDING, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.O.FISCHMANN REVDAT 3 28-FEB-24 3U9N 1 REMARK REVDAT 2 01-FEB-12 3U9N 1 JRNL REVDAT 1 25-JAN-12 3U9N 0 JRNL AUTH X.HUANG,C.C.CHENG,T.O.FISCHMANN,J.S.DUCA,X.YANG,M.RICHARDS, JRNL AUTH 2 G.W.SHIPPS JR. JRNL TITL DISCOVERY OF A NOVEL SERIES OF CHK1 KINASE INHIBITORS WITH JRNL TITL 2 DISTINCTIVE HINGE BINDING MODE JRNL REF ACS MED.CHEM.LETT. 2012 JRNL REFN ISSN 1948-5875 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24314 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1253 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.90 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) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2460 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 : 2090 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.60 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.70 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 3U9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 200 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 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 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: TNT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: .1 M TRIS-CL PH 7.5, 1% V/V N-BUTANOL, REMARK 280 2.5% V/V DMSO, 25% V/V GLYCEROL, 6-12% PEG 3.25K, 2.5 MM TCEP-CL, REMARK 280 10 MM NA2-DITHIONITE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 32.84000 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 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 PRO A 4 REMARK 465 PHE A 5 REMARK 465 VAL A 6 REMARK 465 MET A 42 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 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 ASP A 41 C O CB CG OD1 OD2 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 ARG A 29 23.58 -69.47 REMARK 500 VAL A 30 -70.02 -131.46 REMARK 500 VAL A 40 -113.62 -109.48 REMARK 500 ASP A 99 -3.71 72.69 REMARK 500 ASP A 130 44.68 -149.78 REMARK 500 ASP A 148 89.35 66.97 REMARK 500 ASN A 165 -14.70 -148.02 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 09H A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PA3 RELATED DB: PDB REMARK 900 RELATED ID: 3PA4 RELATED DB: PDB REMARK 900 RELATED ID: 3PA5 RELATED DB: PDB DBREF 3U9N 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 09H A 301 29 HETNAM 09H 2-(2,3-DIHYDRO-1-BENZOFURAN-5-YL)-N-[2-(PIPERAZIN-1- HETNAM 2 09H YL)PHENYL]-1,3-THIAZOLE-4-CARBOXAMIDE FORMUL 2 09H C22 H22 N4 O2 S FORMUL 3 HOH *172(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 THR A 170 ALA A 175 5 6 HELIX 5 5 PRO A 176 ARG A 181 1 6 HELIX 6 6 HIS A 185 GLY A 204 1 20 HELIX 7 7 CYS A 215 GLU A 223 1 9 HELIX 8 8 PRO A 230 ILE A 234 5 5 HELIX 9 9 ASP A 235 LEU A 246 1 12 HELIX 10 10 THR A 255 LYS A 260 1 6 SHEET 1 A 5 TRP A 9 GLY A 18 0 SHEET 2 A 5 GLY A 21 ASN A 28 -1 O VAL A 23 N GLY A 16 SHEET 3 A 5 ALA A 34 ILE A 39 -1 O ILE A 39 N GLU A 22 SHEET 4 A 5 ILE A 79 LEU A 84 -1 O LEU A 84 N ALA A 36 SHEET 5 A 5 PHE A 70 GLU A 76 -1 N TYR A 71 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 3.70 SITE 1 AC1 14 LEU A 15 TYR A 20 ALA A 36 VAL A 68 SITE 2 AC1 14 LEU A 84 GLU A 85 CYS A 87 GLU A 91 SITE 3 AC1 14 GLU A 134 LEU A 137 SER A 147 ASP A 148 SITE 4 AC1 14 HOH A 435 HOH A 498 CRYST1 45.160 65.680 54.780 90.00 102.63 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 0.022143 0.000000 0.004962 0.00000 SCALE2 0.000000 0.015225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018708 0.00000