HEADER TRANSFERASE 14-NOV-17 6EZ6 TITLE PI3 KINASE DELTA IN COMPLEX WITH METHYL 5-(4-(5-((4- TITLE 2 ISOPROPYLPIPERAZIN-1-YL)METHYL)OXAZOL-2-YL)-1H-INDAZOL-6-YL)-2- TITLE 3 METHOXYNICOTINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC COMPND 3 SUBUNIT DELTA ISOFORM; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- COMPND 6 BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA; COMPND 7 EC: 2.7.1.153; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PIK3CD; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS COVALENT INHIBITOR, KINASE, DRUG DISCOVERY, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.CONVERY,S.CAMPOS,S.E.DALTON REVDAT 3 31-JAN-18 6EZ6 1 JRNL REVDAT 2 17-JAN-18 6EZ6 1 JRNL REVDAT 1 27-DEC-17 6EZ6 0 JRNL AUTH S.E.DALTON,L.DITTUS,D.A.THOMAS,M.A.CONVERY,J.NUNES,J.T.BUSH, JRNL AUTH 2 J.P.EVANS,T.WERNER,M.BANTSCHEFF,J.A.MURPHY,S.CAMPOS JRNL TITL SELECTIVELY TARGETING THE KINOME-CONSERVED LYSINE OF PI3K JRNL TITL 2 DELTA AS A GENERAL APPROACH TO COVALENT KINASE INHIBITION. JRNL REF J. AM. CHEM. SOC. V. 140 932 2018 JRNL REFN ESSN 1520-5126 JRNL PMID 29232121 JRNL DOI 10.1021/JACS.7B08979 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.6 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 64648 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 3190 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.23 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4662 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2251 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4443 REMARK 3 BIN R VALUE (WORKING SET) : 0.2237 REMARK 3 BIN FREE R VALUE : 0.2532 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 219 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 : 6944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 483 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69530 REMARK 3 B22 (A**2) : -3.70500 REMARK 3 B33 (A**2) : 3.00960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.36370 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.245 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.176 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.151 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.173 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.150 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 : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7135 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9636 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2534 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 177 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1016 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 7135 ; 20.000 ; HARMONIC 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 : 885 ; 5.000 ; SEMIHARMONIC 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 : 8328 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.83 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.59 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -20.2948 -14.4495 28.8303 REMARK 3 T TENSOR REMARK 3 T11: -0.1473 T22: -0.1623 REMARK 3 T33: -0.1419 T12: 0.0506 REMARK 3 T13: 0.0024 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.7770 L22: 0.6077 REMARK 3 L33: 1.4165 L12: -0.1137 REMARK 3 L13: 0.0239 L23: 0.2565 REMARK 3 S TENSOR REMARK 3 S11: -0.0347 S12: 0.0617 S13: 0.0845 REMARK 3 S21: 0.0563 S22: -0.0405 S23: 0.0426 REMARK 3 S31: -0.0401 S32: -0.3297 S33: 0.0751 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64648 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 58.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.59100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: BUSTER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS CONDITION: 0.1 M BUFFER REMARK 280 SYSTEM 1 PH 6.5, 0.1 M CARBOXYLIC ACIDS, 30% ETHYLENE GLYCOL/PEG REMARK 280 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.26000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.26000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.17500 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: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 MET A -6 REMARK 465 PRO A -5 REMARK 465 PRO A -4 REMARK 465 GLY A -3 REMARK 465 VAL A -2 REMARK 465 ASP A -1 REMARK 465 CYS A 0 REMARK 465 PRO A 1 REMARK 465 MET A 2 REMARK 465 GLU A 3 REMARK 465 PHE A 4 REMARK 465 TRP A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 GLU A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 REMARK 465 GLN A 11 REMARK 465 SER A 12 REMARK 465 VAL A 13 REMARK 465 VAL A 14 REMARK 465 VAL A 15 REMARK 465 ASP A 16 REMARK 465 PHE A 17 REMARK 465 LEU A 18 REMARK 465 LEU A 19 REMARK 465 PRO A 20 REMARK 465 THR A 21 REMARK 465 GLY A 22 REMARK 465 VAL A 23 REMARK 465 TYR A 24 REMARK 465 LEU A 25 REMARK 465 ASN A 26 REMARK 465 PHE A 27 REMARK 465 PRO A 28 REMARK 465 VAL A 29 REMARK 465 SER A 30 REMARK 465 ARG A 31 REMARK 465 ASN A 32 REMARK 465 ALA A 33 REMARK 465 ASN A 34 REMARK 465 LEU A 35 REMARK 465 SER A 36 REMARK 465 THR A 37 REMARK 465 ILE A 38 REMARK 465 LYS A 39 REMARK 465 GLN A 40 REMARK 465 VAL A 41 REMARK 465 LEU A 42 REMARK 465 TRP A 43 REMARK 465 HIS A 44 REMARK 465 ARG A 45 REMARK 465 ALA A 46 REMARK 465 GLN A 47 REMARK 465 TYR A 48 REMARK 465 GLU A 49 REMARK 465 PRO A 50 REMARK 465 LEU A 51 REMARK 465 PHE A 52 REMARK 465 HIS A 53 REMARK 465 MET A 54 REMARK 465 LEU A 55 REMARK 465 SER A 56 REMARK 465 ASP A 57 REMARK 465 PRO A 58 REMARK 465 GLU A 59 REMARK 465 ALA A 60 REMARK 465 TYR A 61 REMARK 465 VAL A 62 REMARK 465 PHE A 63 REMARK 465 THR A 64 REMARK 465 CYS A 65 REMARK 465 VAL A 66 REMARK 465 ASN A 67 REMARK 465 GLN A 68 REMARK 465 THR A 69 REMARK 465 ALA A 70 REMARK 465 GLU A 71 REMARK 465 GLN A 72 REMARK 465 GLN A 73 REMARK 465 GLU A 74 REMARK 465 LEU A 75 REMARK 465 GLU A 76 REMARK 465 ASP A 77 REMARK 465 GLU A 78 REMARK 465 GLN A 79 REMARK 465 ARG A 80 REMARK 465 ARG A 81 REMARK 465 LEU A 82 REMARK 465 CYS A 83 REMARK 465 ASP A 84 REMARK 465 ILE A 85 REMARK 465 GLN A 86 REMARK 465 PRO A 87 REMARK 465 PHE A 88 REMARK 465 LEU A 89 REMARK 465 PRO A 90 REMARK 465 VAL A 91 REMARK 465 LEU A 92 REMARK 465 ARG A 93 REMARK 465 LEU A 94 REMARK 465 VAL A 95 REMARK 465 ALA A 96 REMARK 465 ARG A 97 REMARK 465 GLU A 98 REMARK 465 GLU A 99 REMARK 465 ASN A 100 REMARK 465 LEU A 101 REMARK 465 TYR A 102 REMARK 465 PHE A 103 REMARK 465 GLN A 104 REMARK 465 GLY A 105 REMARK 465 GLY A 106 REMARK 465 TRP A 178 REMARK 465 ARG A 179 REMARK 465 ALA A 180 REMARK 465 GLY A 181 REMARK 465 LEU A 182 REMARK 465 LEU A 183 REMARK 465 ARG A 184 REMARK 465 VAL A 185 REMARK 465 SER A 186 REMARK 465 PRO A 294 REMARK 465 GLN A 295 REMARK 465 VAL A 296 REMARK 465 GLN A 297 REMARK 465 LYS A 298 REMARK 465 PRO A 299 REMARK 465 ARG A 300 REMARK 465 ALA A 301 REMARK 465 LYS A 302 REMARK 465 PRO A 303 REMARK 465 PRO A 304 REMARK 465 PRO A 305 REMARK 465 ILE A 306 REMARK 465 PRO A 307 REMARK 465 ALA A 308 REMARK 465 LYS A 309 REMARK 465 LYS A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 SER A 313 REMARK 465 VAL A 314 REMARK 465 GLU A 399 REMARK 465 LYS A 400 REMARK 465 ALA A 401 REMARK 465 LYS A 402 REMARK 465 LYS A 403 REMARK 465 ALA A 404 REMARK 465 ARG A 405 REMARK 465 SER A 406 REMARK 465 THR A 407 REMARK 465 LYS A 408 REMARK 465 LYS A 409 REMARK 465 LYS A 410 REMARK 465 SER A 411 REMARK 465 LYS A 412 REMARK 465 LYS A 413 REMARK 465 ALA A 414 REMARK 465 PRO A 446 REMARK 465 ASP A 447 REMARK 465 GLU A 448 REMARK 465 LYS A 449 REMARK 465 GLY A 450 REMARK 465 GLU A 451 REMARK 465 ARG A 518 REMARK 465 GLY A 519 REMARK 465 SER A 520 REMARK 465 PHE A 919 REMARK 465 LYS A 920 REMARK 465 THR A 921 REMARK 465 LYS A 922 REMARK 465 PHE A 923 REMARK 465 GLY A 924 REMARK 465 ILE A 925 REMARK 465 ASN A 926 REMARK 465 TRP A 1033 REMARK 465 LEU A 1034 REMARK 465 ALA A 1035 REMARK 465 HIS A 1036 REMARK 465 ASN A 1037 REMARK 465 VAL A 1038 REMARK 465 SER A 1039 REMARK 465 LYS A 1040 REMARK 465 ASP A 1041 REMARK 465 ASN A 1042 REMARK 465 ARG A 1043 REMARK 465 GLN A 1044 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 ARG A 502 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 927 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 928 CG CD OE1 OE2 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 ASN A 244 122.54 -39.93 REMARK 500 ILE A 328 -75.13 -80.87 REMARK 500 ILE A 418 -62.05 -105.48 REMARK 500 SER A 675 88.59 -158.35 REMARK 500 ASP A 736 104.93 -162.97 REMARK 500 GLU A 742 -91.07 -87.88 REMARK 500 ASP A 911 75.11 55.02 REMARK 500 ASN A 949 71.78 -152.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1683 DISTANCE = 6.45 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5Z A 1101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6EYZ RELATED DB: PDB REMARK 900 THE OTHER STRUCTURE IN THE PAPER DBREF 6EZ6 A -6 1044 UNP O35904 PK3CD_MOUSE 1 1043 SEQADV 6EZ6 GLU A 99 UNP O35904 INSERTION SEQADV 6EZ6 ASN A 100 UNP O35904 INSERTION SEQADV 6EZ6 LEU A 101 UNP O35904 INSERTION SEQADV 6EZ6 TYR A 102 UNP O35904 INSERTION SEQADV 6EZ6 PHE A 103 UNP O35904 INSERTION SEQADV 6EZ6 GLN A 104 UNP O35904 INSERTION SEQADV 6EZ6 GLY A 105 UNP O35904 INSERTION SEQADV 6EZ6 GLN A 508 UNP O35904 INSERTION SEQRES 1 A 1051 MET PRO PRO GLY VAL ASP CYS PRO MET GLU PHE TRP THR SEQRES 2 A 1051 LYS GLU GLU SER GLN SER VAL VAL VAL ASP PHE LEU LEU SEQRES 3 A 1051 PRO THR GLY VAL TYR LEU ASN PHE PRO VAL SER ARG ASN SEQRES 4 A 1051 ALA ASN LEU SER THR ILE LYS GLN VAL LEU TRP HIS ARG SEQRES 5 A 1051 ALA GLN TYR GLU PRO LEU PHE HIS MET LEU SER ASP PRO SEQRES 6 A 1051 GLU ALA TYR VAL PHE THR CYS VAL ASN GLN THR ALA GLU SEQRES 7 A 1051 GLN GLN GLU LEU GLU ASP GLU GLN ARG ARG LEU CYS ASP SEQRES 8 A 1051 ILE GLN PRO PHE LEU PRO VAL LEU ARG LEU VAL ALA ARG SEQRES 9 A 1051 GLU GLU ASN LEU TYR PHE GLN GLY GLY ASP ARG VAL LYS SEQRES 10 A 1051 LYS LEU ILE ASN SER GLN ILE SER LEU LEU ILE GLY LYS SEQRES 11 A 1051 GLY LEU HIS GLU PHE ASP SER LEU ARG ASP PRO GLU VAL SEQRES 12 A 1051 ASN ASP PHE ARG THR LYS MET ARG GLN PHE CYS GLU GLU SEQRES 13 A 1051 ALA ALA ALA HIS ARG GLN GLN LEU GLY TRP VAL GLU TRP SEQRES 14 A 1051 LEU GLN TYR SER PHE PRO LEU GLN LEU GLU PRO SER ALA SEQRES 15 A 1051 ARG GLY TRP ARG ALA GLY LEU LEU ARG VAL SER ASN ARG SEQRES 16 A 1051 ALA LEU LEU VAL ASN VAL LYS PHE GLU GLY SER GLU GLU SEQRES 17 A 1051 SER PHE THR PHE GLN VAL SER THR LYS ASP MET PRO LEU SEQRES 18 A 1051 ALA LEU MET ALA CYS ALA LEU ARG LYS LYS ALA THR VAL SEQRES 19 A 1051 PHE ARG GLN PRO LEU VAL GLU GLN PRO GLU GLU TYR ALA SEQRES 20 A 1051 LEU GLN VAL ASN GLY ARG HIS GLU TYR LEU TYR GLY ASN SEQRES 21 A 1051 TYR PRO LEU CYS HIS PHE GLN TYR ILE CYS SER CYS LEU SEQRES 22 A 1051 HIS SER GLY LEU THR PRO HIS LEU THR MET VAL HIS SER SEQRES 23 A 1051 SER SER ILE LEU ALA MET ARG ASP GLU GLN SER ASN PRO SEQRES 24 A 1051 ALA PRO GLN VAL GLN LYS PRO ARG ALA LYS PRO PRO PRO SEQRES 25 A 1051 ILE PRO ALA LYS LYS PRO SER SER VAL SER LEU TRP SER SEQRES 26 A 1051 LEU GLU GLN PRO PHE SER ILE GLU LEU ILE GLU GLY ARG SEQRES 27 A 1051 LYS VAL ASN ALA ASP GLU ARG MET LYS LEU VAL VAL GLN SEQRES 28 A 1051 ALA GLY LEU PHE HIS GLY ASN GLU MET LEU CYS LYS THR SEQRES 29 A 1051 VAL SER SER SER GLU VAL ASN VAL CYS SER GLU PRO VAL SEQRES 30 A 1051 TRP LYS GLN ARG LEU GLU PHE ASP ILE SER VAL CYS ASP SEQRES 31 A 1051 LEU PRO ARG MET ALA ARG LEU CYS PHE ALA LEU TYR ALA SEQRES 32 A 1051 VAL VAL GLU LYS ALA LYS LYS ALA ARG SER THR LYS LYS SEQRES 33 A 1051 LYS SER LYS LYS ALA ASP CYS PRO ILE ALA TRP ALA ASN SEQRES 34 A 1051 LEU MET LEU PHE ASP TYR LYS ASP GLN LEU LYS THR GLY SEQRES 35 A 1051 GLU ARG CYS LEU TYR MET TRP PRO SER VAL PRO ASP GLU SEQRES 36 A 1051 LYS GLY GLU LEU LEU ASN PRO ALA GLY THR VAL ARG GLY SEQRES 37 A 1051 ASN PRO ASN THR GLU SER ALA ALA ALA LEU VAL ILE TYR SEQRES 38 A 1051 LEU PRO GLU VAL ALA PRO HIS PRO VAL TYR PHE PRO ALA SEQRES 39 A 1051 LEU GLU LYS ILE LEU GLU LEU GLY ARG HIS GLY GLU ARG SEQRES 40 A 1051 GLY ARG ILE THR GLU GLU GLU GLN LEU GLN LEU ARG GLU SEQRES 41 A 1051 ILE LEU GLU ARG ARG GLY SER GLY GLU LEU TYR GLU HIS SEQRES 42 A 1051 GLU LYS ASP LEU VAL TRP LYS MET ARG HIS GLU VAL GLN SEQRES 43 A 1051 GLU HIS PHE PRO GLU ALA LEU ALA ARG LEU LEU LEU VAL SEQRES 44 A 1051 THR LYS TRP ASN LYS HIS GLU ASP VAL ALA GLN MET LEU SEQRES 45 A 1051 TYR LEU LEU CYS SER TRP PRO GLU LEU PRO VAL LEU SER SEQRES 46 A 1051 ALA LEU GLU LEU LEU ASP PHE SER PHE PRO ASP CYS TYR SEQRES 47 A 1051 VAL GLY SER PHE ALA ILE LYS SER LEU ARG LYS LEU THR SEQRES 48 A 1051 ASP ASP GLU LEU PHE GLN TYR LEU LEU GLN LEU VAL GLN SEQRES 49 A 1051 VAL LEU LYS TYR GLU SER TYR LEU ASP CYS GLU LEU THR SEQRES 50 A 1051 LYS PHE LEU LEU GLY ARG ALA LEU ALA ASN ARG LYS ILE SEQRES 51 A 1051 GLY HIS PHE LEU PHE TRP HIS LEU ARG SER GLU MET HIS SEQRES 52 A 1051 VAL PRO SER VAL ALA LEU ARG PHE GLY LEU ILE MET GLU SEQRES 53 A 1051 ALA TYR CYS ARG GLY SER THR HIS HIS MET LYS VAL LEU SEQRES 54 A 1051 MET LYS GLN GLY GLU ALA LEU SER LYS LEU LYS ALA LEU SEQRES 55 A 1051 ASN ASP PHE VAL LYS VAL SER SER GLN LYS THR THR LYS SEQRES 56 A 1051 PRO GLN THR LYS GLU MET MET HIS MET CYS MET ARG GLN SEQRES 57 A 1051 GLU THR TYR MET GLU ALA LEU SER HIS LEU GLN SER PRO SEQRES 58 A 1051 LEU ASP PRO SER THR LEU LEU GLU GLU VAL CYS VAL GLU SEQRES 59 A 1051 GLN CYS THR PHE MET ASP SER LYS MET LYS PRO LEU TRP SEQRES 60 A 1051 ILE MET TYR SER SER GLU GLU ALA GLY SER ALA GLY ASN SEQRES 61 A 1051 VAL GLY ILE ILE PHE LYS ASN GLY ASP ASP LEU ARG GLN SEQRES 62 A 1051 ASP MET LEU THR LEU GLN MET ILE GLN LEU MET ASP VAL SEQRES 63 A 1051 LEU TRP LYS GLN GLU GLY LEU ASP LEU ARG MET THR PRO SEQRES 64 A 1051 TYR GLY CYS LEU PRO THR GLY ASP ARG THR GLY LEU ILE SEQRES 65 A 1051 GLU VAL VAL LEU HIS SER ASP THR ILE ALA ASN ILE GLN SEQRES 66 A 1051 LEU ASN LYS SER ASN MET ALA ALA THR ALA ALA PHE ASN SEQRES 67 A 1051 LYS ASP ALA LEU LEU ASN TRP LEU LYS SER LYS ASN PRO SEQRES 68 A 1051 GLY GLU ALA LEU ASP ARG ALA ILE GLU GLU PHE THR LEU SEQRES 69 A 1051 SER CYS ALA GLY TYR CYS VAL ALA THR TYR VAL LEU GLY SEQRES 70 A 1051 ILE GLY ASP ARG HIS SER ASP ASN ILE MET ILE ARG GLU SEQRES 71 A 1051 SER GLY GLN LEU PHE HIS ILE ASP PHE GLY HIS PHE LEU SEQRES 72 A 1051 GLY ASN PHE LYS THR LYS PHE GLY ILE ASN ARG GLU ARG SEQRES 73 A 1051 VAL PRO PHE ILE LEU THR TYR ASP PHE VAL HIS VAL ILE SEQRES 74 A 1051 GLN GLN GLY LYS THR ASN ASN SER GLU LYS PHE GLU ARG SEQRES 75 A 1051 PHE ARG GLY TYR CYS GLU ARG ALA TYR THR ILE LEU ARG SEQRES 76 A 1051 ARG HIS GLY LEU LEU PHE LEU HIS LEU PHE ALA LEU MET SEQRES 77 A 1051 ARG ALA ALA GLY LEU PRO GLU LEU SER CYS SER LYS ASP SEQRES 78 A 1051 ILE GLN TYR LEU LYS ASP SER LEU ALA LEU GLY LYS THR SEQRES 79 A 1051 GLU GLU GLU ALA LEU LYS HIS PHE ARG VAL LYS PHE ASN SEQRES 80 A 1051 GLU ALA LEU ARG GLU SER TRP LYS THR LYS VAL ASN TRP SEQRES 81 A 1051 LEU ALA HIS ASN VAL SER LYS ASP ASN ARG GLN HET C5Z A1101 36 HETNAM C5Z METHYL 2-METHOXY-5-[4-[5-[(4-PROPAN-2-YLPIPERAZIN-1- HETNAM 2 C5Z YL)METHYL]-1,3-OXAZOL-2-YL]-2~{H}-INDAZOL-6- HETNAM 3 C5Z YL]PYRIDINE-3-CARBOXYLATE FORMUL 2 C5Z C26 H30 N6 O4 FORMUL 3 HOH *483(H2 O) HELIX 1 AA1 ASP A 107 GLY A 122 1 16 HELIX 2 AA2 LEU A 125 LEU A 131 1 7 HELIX 3 AA3 ASP A 133 GLN A 155 1 23 HELIX 4 AA4 GLY A 158 PHE A 167 1 10 HELIX 5 AA5 GLU A 172 ARG A 176 5 5 HELIX 6 AA6 MET A 212 PHE A 228 1 17 HELIX 7 AA7 GLN A 235 GLU A 237 5 3 HELIX 8 AA8 PRO A 255 HIS A 258 5 4 HELIX 9 AA9 PHE A 259 GLY A 269 1 11 HELIX 10 AB1 SER A 279 GLN A 289 1 11 HELIX 11 AB2 SER A 315 LEU A 319 5 5 HELIX 12 AB3 CYS A 382 LEU A 384 5 3 HELIX 13 AB4 ALA A 487 HIS A 497 1 11 HELIX 14 AB5 THR A 504 ARG A 517 1 14 HELIX 15 AB6 TYR A 524 MET A 534 1 11 HELIX 16 AB7 MET A 534 PHE A 542 1 9 HELIX 17 AB8 ALA A 545 THR A 553 1 9 HELIX 18 AB9 LYS A 557 CYS A 569 1 13 HELIX 19 AC1 PRO A 575 LEU A 583 1 9 HELIX 20 AC2 ASP A 589 ARG A 601 1 13 HELIX 21 AC3 THR A 604 LEU A 619 1 16 HELIX 22 AC4 LYS A 620 GLU A 622 5 3 HELIX 23 AC5 CYS A 627 ASN A 640 1 14 HELIX 24 AC6 ASN A 640 SER A 653 1 14 HELIX 25 AC7 VAL A 657 SER A 675 1 19 HELIX 26 AC8 SER A 675 SER A 703 1 29 HELIX 27 AC9 THR A 707 ARG A 720 1 14 HELIX 28 AD1 GLN A 721 SER A 729 1 9 HELIX 29 AD2 VAL A 746 CYS A 749 5 4 HELIX 30 AD3 ALA A 768 ASN A 773 5 6 HELIX 31 AD4 LEU A 784 GLU A 804 1 21 HELIX 32 AD5 ILE A 834 LEU A 839 1 6 HELIX 33 AD6 PHE A 850 LYS A 852 5 3 HELIX 34 AD7 ASP A 853 ASN A 863 1 11 HELIX 35 AD8 GLU A 866 GLY A 890 1 25 HELIX 36 AD9 HIS A 895 ASP A 897 5 3 HELIX 37 AE1 THR A 935 GLN A 943 1 9 HELIX 38 AE2 ASN A 949 HIS A 970 1 22 HELIX 39 AE3 HIS A 970 ARG A 982 1 13 HELIX 40 AE4 ALA A 983 GLY A 985 5 3 HELIX 41 AE5 CYS A 991 LEU A 1002 1 12 HELIX 42 AE6 THR A 1007 VAL A 1031 1 25 SHEET 1 AA1 5 SER A 202 SER A 208 0 SHEET 2 AA1 5 ALA A 189 PHE A 196 -1 N VAL A 194 O PHE A 203 SHEET 3 AA1 5 HIS A 273 HIS A 278 1 O LEU A 274 N ASN A 193 SHEET 4 AA1 5 TYR A 239 VAL A 243 -1 N ALA A 240 O VAL A 277 SHEET 5 AA1 5 TYR A 249 LEU A 250 -1 O LEU A 250 N LEU A 241 SHEET 1 AA2 4 VAL A 370 SER A 380 0 SHEET 2 AA2 4 PRO A 322 ARG A 331 -1 N PHE A 323 O PHE A 377 SHEET 3 AA2 4 ALA A 470 LEU A 475 -1 O VAL A 472 N GLU A 329 SHEET 4 AA2 4 GLY A 435 TYR A 440 -1 N LEU A 439 O LEU A 471 SHEET 1 AA3 3 GLU A 352 MET A 353 0 SHEET 2 AA3 3 LYS A 340 HIS A 349 -1 N HIS A 349 O GLU A 352 SHEET 3 AA3 3 VAL A 363 ASN A 364 -1 O VAL A 363 N LEU A 341 SHEET 1 AA4 5 VAL A 358 SER A 359 0 SHEET 2 AA4 5 LYS A 340 HIS A 349 -1 N ALA A 345 O VAL A 358 SHEET 3 AA4 5 ARG A 389 VAL A 397 -1 O CYS A 391 N GLY A 346 SHEET 4 AA4 5 CYS A 416 MET A 424 -1 O LEU A 423 N LEU A 390 SHEET 5 AA4 5 TRP A 442 PRO A 443 -1 O TRP A 442 N TRP A 420 SHEET 1 AA5 2 LEU A 731 SER A 733 0 SHEET 2 AA5 2 ASP A 736 LEU A 741 -1 O LEU A 741 N LEU A 731 SHEET 1 AA6 3 GLU A 743 VAL A 744 0 SHEET 2 AA6 3 LEU A 759 SER A 764 -1 O SER A 764 N GLU A 743 SHEET 3 AA6 3 THR A 750 PHE A 751 -1 N THR A 750 O TRP A 760 SHEET 1 AA7 5 GLU A 743 VAL A 744 0 SHEET 2 AA7 5 LEU A 759 SER A 764 -1 O SER A 764 N GLU A 743 SHEET 3 AA7 5 VAL A 774 ASN A 780 -1 O ILE A 776 N ILE A 761 SHEET 4 AA7 5 THR A 822 GLU A 826 -1 O ILE A 825 N ILE A 777 SHEET 5 AA7 5 CYS A 815 GLY A 819 -1 N LEU A 816 O LEU A 824 SHEET 1 AA8 3 SER A 831 THR A 833 0 SHEET 2 AA8 3 ILE A 899 ARG A 902 -1 O ILE A 901 N ASP A 832 SHEET 3 AA8 3 LEU A 907 HIS A 909 -1 O PHE A 908 N MET A 900 SITE 1 AC1 17 THR A 750 SER A 754 TRP A 760 ILE A 777 SITE 2 AC1 17 LYS A 779 LEU A 784 ASP A 787 GLU A 826 SITE 3 AC1 17 VAL A 827 VAL A 828 ASP A 832 MET A 900 SITE 4 AC1 17 ILE A 910 ASP A 911 HOH A1224 HOH A1232 SITE 5 AC1 17 HOH A1464 CRYST1 142.520 64.350 116.190 90.00 103.01 90.00 C 1 2 1 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 0.007017 0.000000 0.001621 0.00000 SCALE2 0.000000 0.015540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008833 0.00000