HEADER TRANSFERASE 24-FEB-16 5IDP TITLE CDK8-CYCC IN COMPLEX WITH (3-AMINO-1H-INDAZOL-5-YL)-[(S)-2-(4-FLUORO- TITLE 2 PHENYL)-PIPERIDIN-1-YL]-METHANONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 3-405; COMPND 5 SYNONYM: CELL DIVISION PROTEIN KINASE 8,MEDIATOR COMPLEX SUBUNIT COMPND 6 CDK8,MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8,PROTEIN COMPND 7 KINASE K35; COMPND 8 EC: 2.7.11.22,2.7.11.23; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: CYCLIN-C; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: SRB11 HOMOLOG,HSRB11; COMPND 14 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: CDK8; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CCNC; SOURCE 14 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 15 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CDK8 KINASE / CYCLIN C, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.MUSIL,J.BLAGG,A.MALLINGER,P.CZODROWSKI,K.SCHIEMANN REVDAT 2 10-JAN-24 5IDP 1 REMARK REVDAT 1 21-DEC-16 5IDP 0 JRNL AUTH P.CZODROWSKI,A.MALLINGER,D.WIENKE,C.ESDAR,O.POSCHKE,M.BUSCH, JRNL AUTH 2 F.ROHDICH,S.A.ECCLES,M.J.ORTIZ-RUIZ,R.SCHNEIDER,F.I.RAYNAUD, JRNL AUTH 3 P.A.CLARKE,D.MUSIL,D.SCHWARZ,T.DALE,K.URBAHNS,J.BLAGG, JRNL AUTH 4 K.SCHIEMANN JRNL TITL STRUCTURE-BASED OPTIMIZATION OF POTENT, SELECTIVE, AND JRNL TITL 2 ORALLY BIOAVAILABLE CDK8 INHIBITORS DISCOVERED BY JRNL TITL 3 HIGH-THROUGHPUT SCREENING. JRNL REF J. MED. CHEM. V. 59 9337 2016 JRNL REFN ISSN 1520-4804 JRNL PMID 27490956 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00597 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 24027 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT : 855 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1713 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.4150 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : -1.78000 REMARK 3 B33 (A**2) : 1.50000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.682 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.337 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.253 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.769 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5013 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4712 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6807 ; 1.173 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10755 ; 2.589 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 606 ; 5.527 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;31.886 ;23.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 803 ;11.866 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.937 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 749 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5621 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1196 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2437 ; 2.218 ; 3.181 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2438 ; 2.218 ; 3.182 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3038 ; 3.658 ; 5.349 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3039 ; 3.658 ; 5.351 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2576 ; 2.425 ; 3.369 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2567 ; 2.375 ; 3.356 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3770 ; 3.828 ; 5.572 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5552 ; 5.758 ;14.130 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5547 ; 5.756 ;14.126 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5IDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24882 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 86.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 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: REFMAC REMARK 200 STARTING MODEL: 4F6S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M SODIUM FORMATE, PH REMARK 280 6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 35.55650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.16750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.54650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 86.16750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.55650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.54650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A -1 REMARK 465 ALA A 116 REMARK 465 ASN A 117 REMARK 465 LYS A 118 REMARK 465 LYS A 119 REMARK 465 PRO A 120 REMARK 465 PRO A 186 REMARK 465 LEU A 187 REMARK 465 ALA A 188 REMARK 465 ASP A 189 REMARK 465 LEU A 190 REMARK 465 ASP A 191 REMARK 465 PRO A 192 REMARK 465 VAL A 193 REMARK 465 VAL A 194 REMARK 465 VAL A 195 REMARK 465 ASP A 240 REMARK 465 ILE A 241 REMARK 465 LYS A 242 REMARK 465 THR A 360 REMARK 465 GLU A 361 REMARK 465 GLU A 362 REMARK 465 GLU A 363 REMARK 465 PRO A 364 REMARK 465 PRO A 365 REMARK 465 LEU A 366 REMARK 465 LYS A 367 REMARK 465 LYS A 368 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 0 CG CD CE NZ REMARK 480 LYS A 6 CD CE NZ REMARK 480 GLU A 23 CG CD OE1 OE2 REMARK 480 LYS A 39 CG CD CE NZ REMARK 480 ARG A 40 NE CZ NH1 NH2 REMARK 480 ASP A 42 CG OD1 OD2 REMARK 480 LYS A 44 CG CD CE NZ REMARK 480 ASP A 45 CG OD1 OD2 REMARK 480 ASP A 46 CG OD1 OD2 REMARK 480 LYS A 47 CG CD CE NZ REMARK 480 LYS A 74 CG CD CE NZ REMARK 480 LYS A 83 CD CE NZ REMARK 480 LYS A 92 NZ REMARK 480 LYS A 109 CD CE NZ REMARK 480 ARG A 112 CZ NH1 NH2 REMARK 480 SER A 114 OG REMARK 480 LYS A 115 N CA CG CD CE NZ REMARK 480 VAL A 121 CG1 CG2 REMARK 480 LEU A 123 CG CD1 CD2 REMARK 480 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 185 CG CD CE NZ REMARK 480 ARG A 209 CD NE CZ NH1 NH2 REMARK 480 ARG A 237 CG CD NE CZ NH1 NH2 REMARK 480 GLN A 238 CG CD OE1 NE2 REMARK 480 GLU A 239 CG CD OE1 OE2 REMARK 480 SER A 244 OG REMARK 480 LYS A 265 CE NZ REMARK 480 LYS A 271 CG CD CE NZ REMARK 480 LYS A 272 CD CE NZ REMARK 480 LYS A 281 CD CE NZ REMARK 480 ASN A 286 CG OD1 ND2 REMARK 480 ASN A 290 CG OD1 ND2 REMARK 480 LYS A 295 CD CE NZ REMARK 480 LYS A 299 CD CE NZ REMARK 480 LYS A 301 CD CE NZ REMARK 480 LYS A 303 CD CE NZ REMARK 480 GLU A 327 CD OE1 OE2 REMARK 480 GLN A 350 CG CD OE1 NE2 REMARK 480 LYS A 355 CG CD CE NZ REMARK 480 GLU A 357 CG CD OE1 OE2 REMARK 480 ASP B -2 CG OD1 OD2 REMARK 480 LYS B -1 CD CE NZ REMARK 480 LYS B 18 CD CE NZ REMARK 480 LYS B 23 CD CE NZ REMARK 480 LYS B 30 CG CD CE NZ REMARK 480 TRP B 38 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 480 TRP B 38 CZ3 CH2 REMARK 480 LYS B 56 CD CE NZ REMARK 480 LYS B 79 CE NZ REMARK 480 LYS B 117 CD CE NZ REMARK 480 LYS B 126 CD CE NZ REMARK 480 GLU B 127 CG CD OE1 OE2 REMARK 480 ARG B 131 CG CD NE CZ NH1 NH2 REMARK 480 GLN B 164 CG CD OE1 NE2 REMARK 480 GLU B 169 CD OE1 OE2 REMARK 480 ASP B 170 CG OD1 OD2 REMARK 480 MET B 171 CG SD CE REMARK 480 LYS B 211 CD CE NZ REMARK 480 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 480 SER B 221 OG REMARK 480 GLU B 225 CG CD OE1 OE2 REMARK 480 LYS B 226 NZ REMARK 480 LYS B 236 CD CE NZ REMARK 480 LYS B 256 NZ REMARK 480 LYS B 259 CG CD CE NZ REMARK 480 LYS B 261 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 115 CA LYS A 115 CB 0.221 REMARK 500 LYS A 115 CB LYS A 115 CG -0.236 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 ASP A 151 46.50 -157.84 REMARK 500 PHE A 234 48.88 -109.06 REMARK 500 GLN A 238 91.41 -68.68 REMARK 500 TRP A 267 77.56 -150.67 REMARK 500 LEU A 316 56.02 -95.55 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 6A6 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 303 DBREF 5IDP A 1 364 UNP P49336 CDK8_HUMAN 1 364 DBREF 5IDP B 1 264 UNP P24863 CCNC_HUMAN 1 264 SEQADV 5IDP ASP A -1 UNP P49336 EXPRESSION TAG SEQADV 5IDP LYS A 0 UNP P49336 EXPRESSION TAG SEQADV 5IDP PRO A 365 UNP P49336 EXPRESSION TAG SEQADV 5IDP LEU A 366 UNP P49336 EXPRESSION TAG SEQADV 5IDP LYS A 367 UNP P49336 EXPRESSION TAG SEQADV 5IDP LYS A 368 UNP P49336 EXPRESSION TAG SEQADV 5IDP ASP B -3 UNP P24863 EXPRESSION TAG SEQADV 5IDP ASP B -2 UNP P24863 EXPRESSION TAG SEQADV 5IDP LYS B -1 UNP P24863 EXPRESSION TAG SEQADV 5IDP ALA B 0 UNP P24863 EXPRESSION TAG SEQRES 1 A 370 ASP LYS MET ASP TYR ASP PHE LYS VAL LYS LEU SER SER SEQRES 2 A 370 GLU ARG GLU ARG VAL GLU ASP LEU PHE GLU TYR GLU GLY SEQRES 3 A 370 CYS LYS VAL GLY ARG GLY THR TYR GLY HIS VAL TYR LYS SEQRES 4 A 370 ALA LYS ARG LYS ASP GLY LYS ASP ASP LYS ASP TYR ALA SEQRES 5 A 370 LEU LYS GLN ILE GLU GLY THR GLY ILE SER MET SER ALA SEQRES 6 A 370 CYS ARG GLU ILE ALA LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 7 A 370 ASN VAL ILE SER LEU GLN LYS VAL PHE LEU SER HIS ALA SEQRES 8 A 370 ASP ARG LYS VAL TRP LEU LEU PHE ASP TYR ALA GLU HIS SEQRES 9 A 370 ASP LEU TRP HIS ILE ILE LYS PHE HIS ARG ALA SER LYS SEQRES 10 A 370 ALA ASN LYS LYS PRO VAL GLN LEU PRO ARG GLY MET VAL SEQRES 11 A 370 LYS SER LEU LEU TYR GLN ILE LEU ASP GLY ILE HIS TYR SEQRES 12 A 370 LEU HIS ALA ASN TRP VAL LEU HIS ARG ASP LEU LYS PRO SEQRES 13 A 370 ALA ASN ILE LEU VAL MET GLY GLU GLY PRO GLU ARG GLY SEQRES 14 A 370 ARG VAL LYS ILE ALA ASP MET GLY PHE ALA ARG LEU PHE SEQRES 15 A 370 ASN SER PRO LEU LYS PRO LEU ALA ASP LEU ASP PRO VAL SEQRES 16 A 370 VAL VAL THR PHE TRP TYR ARG ALA PRO GLU LEU LEU LEU SEQRES 17 A 370 GLY ALA ARG HIS TYR THR LYS ALA ILE ASP ILE TRP ALA SEQRES 18 A 370 ILE GLY CYS ILE PHE ALA GLU LEU LEU THR SER GLU PRO SEQRES 19 A 370 ILE PHE HIS CYS ARG GLN GLU ASP ILE LYS THR SER ASN SEQRES 20 A 370 PRO TYR HIS HIS ASP GLN LEU ASP ARG ILE PHE ASN VAL SEQRES 21 A 370 MET GLY PHE PRO ALA ASP LYS ASP TRP GLU ASP ILE LYS SEQRES 22 A 370 LYS MET PRO GLU HIS SER THR LEU MET LYS ASP PHE ARG SEQRES 23 A 370 ARG ASN THR TYR THR ASN CYS SER LEU ILE LYS TYR MET SEQRES 24 A 370 GLU LYS HIS LYS VAL LYS PRO ASP SER LYS ALA PHE HIS SEQRES 25 A 370 LEU LEU GLN LYS LEU LEU THR MET ASP PRO ILE LYS ARG SEQRES 26 A 370 ILE THR SER GLU GLN ALA MET GLN ASP PRO TYR PHE LEU SEQRES 27 A 370 GLU ASP PRO LEU PRO THR SER ASP VAL PHE ALA GLY CYS SEQRES 28 A 370 GLN ILE PRO TYR PRO LYS ARG GLU PHE LEU THR GLU GLU SEQRES 29 A 370 GLU PRO PRO LEU LYS LYS SEQRES 1 B 268 ASP ASP LYS ALA MET ALA GLY ASN PHE TRP GLN SER SER SEQRES 2 B 268 HIS TYR LEU GLN TRP ILE LEU ASP LYS GLN ASP LEU LEU SEQRES 3 B 268 LYS GLU ARG GLN LYS ASP LEU LYS PHE LEU SER GLU GLU SEQRES 4 B 268 GLU TYR TRP LYS LEU GLN ILE PHE PHE THR ASN VAL ILE SEQRES 5 B 268 GLN ALA LEU GLY GLU HIS LEU LYS LEU ARG GLN GLN VAL SEQRES 6 B 268 ILE ALA THR ALA THR VAL TYR PHE LYS ARG PHE TYR ALA SEQRES 7 B 268 ARG TYR SER LEU LYS SER ILE ASP PRO VAL LEU MET ALA SEQRES 8 B 268 PRO THR CYS VAL PHE LEU ALA SER LYS VAL GLU GLU PHE SEQRES 9 B 268 GLY VAL VAL SER ASN THR ARG LEU ILE ALA ALA ALA THR SEQRES 10 B 268 SER VAL LEU LYS THR ARG PHE SER TYR ALA PHE PRO LYS SEQRES 11 B 268 GLU PHE PRO TYR ARG MET ASN HIS ILE LEU GLU CYS GLU SEQRES 12 B 268 PHE TYR LEU LEU GLU LEU MET ASP CYS CYS LEU ILE VAL SEQRES 13 B 268 TYR HIS PRO TYR ARG PRO LEU LEU GLN TYR VAL GLN ASP SEQRES 14 B 268 MET GLY GLN GLU ASP MET LEU LEU PRO LEU ALA TRP ARG SEQRES 15 B 268 ILE VAL ASN ASP THR TYR ARG THR ASP LEU CYS LEU LEU SEQRES 16 B 268 TYR PRO PRO PHE MET ILE ALA LEU ALA CYS LEU HIS VAL SEQRES 17 B 268 ALA CYS VAL VAL GLN GLN LYS ASP ALA ARG GLN TRP PHE SEQRES 18 B 268 ALA GLU LEU SER VAL ASP MET GLU LYS ILE LEU GLU ILE SEQRES 19 B 268 ILE ARG VAL ILE LEU LYS LEU TYR GLU GLN TRP LYS ASN SEQRES 20 B 268 PHE ASP GLU ARG LYS GLU MET ALA THR ILE LEU SER LYS SEQRES 21 B 268 MET PRO LYS PRO LYS PRO PRO PRO HET 6A6 A 401 25 HET FMT A 402 3 HET FMT A 403 3 HET FMT B 301 3 HET FMT B 302 3 HET FMT B 303 3 HETNAM 6A6 (3-AMINO-1H-INDAZOL-5-YL)[(2S)-2-(4-FLUOROPHENYL) HETNAM 2 6A6 PIPERIDIN-1-YL]METHANONE HETNAM FMT FORMIC ACID FORMUL 3 6A6 C19 H19 F N4 O FORMUL 4 FMT 5(C H2 O2) FORMUL 9 HOH *66(H2 O) HELIX 1 AA1 ASP A 2 ARG A 13 1 12 HELIX 2 AA2 ARG A 15 LEU A 19 1 5 HELIX 3 AA3 SER A 60 ARG A 71 1 12 HELIX 4 AA4 LEU A 104 SER A 114 1 11 HELIX 5 AA5 GLY A 126 ASN A 145 1 20 HELIX 6 AA6 LYS A 153 ALA A 155 5 3 HELIX 7 AA7 ARG A 178 SER A 182 5 5 HELIX 8 AA8 ALA A 201 LEU A 206 1 6 HELIX 9 AA9 THR A 212 SER A 230 1 19 HELIX 10 AB1 HIS A 248 GLY A 260 1 13 HELIX 11 AB2 TRP A 267 MET A 273 5 7 HELIX 12 AB3 GLU A 275 PHE A 283 1 9 HELIX 13 AB4 ARG A 284 THR A 289 5 6 HELIX 14 AB5 SER A 292 HIS A 300 1 9 HELIX 15 AB6 SER A 306 LEU A 316 1 11 HELIX 16 AB7 ASP A 319 ARG A 323 5 5 HELIX 17 AB8 THR A 325 GLN A 331 1 7 HELIX 18 AB9 ASP A 332 GLU A 337 5 6 HELIX 19 AC1 ASN B 4 GLN B 7 5 4 HELIX 20 AC2 SER B 8 ILE B 15 1 8 HELIX 21 AC3 ASP B 17 GLN B 26 1 10 HELIX 22 AC4 SER B 33 LEU B 55 1 23 HELIX 23 AC5 ARG B 58 TYR B 76 1 19 HELIX 24 AC6 ASP B 82 GLU B 98 1 17 HELIX 25 AC7 SER B 104 ARG B 119 1 16 HELIX 26 AC8 ARG B 131 MET B 146 1 16 HELIX 27 AC9 PRO B 155 GLY B 167 1 13 HELIX 28 AD1 GLN B 168 TYR B 184 1 17 HELIX 29 AD2 ASP B 187 TYR B 192 1 6 HELIX 30 AD3 PRO B 193 GLN B 209 1 17 HELIX 31 AD4 ALA B 213 LEU B 220 1 8 HELIX 32 AD5 ASP B 223 PHE B 244 1 22 HELIX 33 AD6 ASP B 245 MET B 257 1 13 SHEET 1 AA1 3 PHE A 20 GLU A 21 0 SHEET 2 AA1 3 GLY A 33 ARG A 40 -1 O LYS A 39 N GLU A 21 SHEET 3 AA1 3 LYS A 26 ARG A 29 -1 N GLY A 28 O VAL A 35 SHEET 1 AA2 5 PHE A 20 GLU A 21 0 SHEET 2 AA2 5 GLY A 33 ARG A 40 -1 O LYS A 39 N GLU A 21 SHEET 3 AA2 5 TYR A 49 ILE A 54 -1 O TYR A 49 N ALA A 38 SHEET 4 AA2 5 LYS A 92 ASP A 98 -1 O LEU A 95 N LYS A 52 SHEET 5 AA2 5 LEU A 81 SER A 87 -1 N GLN A 82 O LEU A 96 SHEET 1 AA3 3 HIS A 102 ASP A 103 0 SHEET 2 AA3 3 ILE A 157 VAL A 159 -1 O VAL A 159 N HIS A 102 SHEET 3 AA3 3 VAL A 169 ILE A 171 -1 O LYS A 170 N LEU A 158 CISPEP 1 ASP A 338 PRO A 339 0 4.35 SITE 1 AC1 13 VAL A 27 TYR A 32 VAL A 35 ALA A 50 SITE 2 AC1 13 ASP A 98 TYR A 99 ALA A 100 ASP A 103 SITE 3 AC1 13 ALA A 155 ASP A 173 ARG A 356 FMT A 402 SITE 4 AC1 13 HOH A 510 SITE 1 AC2 3 GLU A 66 ASP A 173 6A6 A 401 SITE 1 AC3 3 LYS A 83 VAL A 84 ASP B 147 SITE 1 AC4 5 GLN B 41 THR B 45 THR B 66 PHE B 69 SITE 2 AC4 5 LYS B 70 SITE 1 AC5 4 GLN B 49 GLN B 59 ALA B 63 TYR B 156 SITE 1 AC6 4 ASP B -2 ALA B 0 ALA B 2 TYR B 153 CRYST1 71.113 71.093 172.335 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 0.014062 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005803 0.00000