HEADER TRANSFERASE/TRANSFERASE INHIBITOR 30-JUL-19 6PYS TITLE HUMAN PI3KALPHA IN COMPLEX WITH COMPOUND 2-10 ((3S)-3-BENZYL-3-METHYL- TITLE 2 5-[5-(2-METHYLPYRIMIDIN-5-YL)PYRAZOLO[1,5-A]PYRIMIDIN-3-YL]-1,3- TITLE 3 DIHYDRO-2H-INDOL-2-ONE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC COMPND 3 SUBUNIT ALPHA ISOFORM; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 107-1051; COMPND 6 SYNONYM: PTDINS-3-KINASE SUBUNIT ALPHA,PHOSPHATIDYLINOSITOL 4,5- COMPND 7 BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT ALPHA,P110ALPHA, COMPND 8 PHOSPHOINOSITIDE-3-KINASE CATALYTIC ALPHA POLYPEPTIDE, COMPND 9 SERINE/THREONINE PROTEIN KINASE PIK3CA; COMPND 10 EC: 2.7.1.153,2.7.11.1; COMPND 11 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: PIK3CA; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PI3KALPHA KINASE, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.A.LESBURG,M.A.AUGUSTIN REVDAT 3 13-MAR-24 6PYS 1 REMARK REVDAT 2 04-SEP-19 6PYS 1 JRNL REVDAT 1 28-AUG-19 6PYS 0 JRNL AUTH X.FRADERA,J.L.METHOT,A.ACHAB,M.CHRISTOPHER,M.D.ALTMAN, JRNL AUTH 2 H.ZHOU,M.A.MCGOWAN,S.D.KATTAR,K.WILSON,Y.GARCIA, JRNL AUTH 3 M.A.AUGUSTIN,C.A.LESBURG,S.SHAH,P.GOLDENBLATT,J.D.KATZ JRNL TITL DESIGN OF SELECTIVE PI3K DELTA INHIBITORS USING AN ITERATIVE JRNL TITL 2 SCAFFOLD-HOPPING WORKFLOW. JRNL REF BIOORG.MED.CHEM.LETT. V. 29 2575 2019 JRNL REFN ESSN 1464-3405 JRNL PMID 31416665 JRNL DOI 10.1016/J.BMCL.2019.08.004 REMARK 2 REMARK 2 RESOLUTION. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 56166 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1498 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4084 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7277 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 2.38000 REMARK 3 B33 (A**2) : -2.87000 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.108 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7291 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6861 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9903 ; 1.052 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15686 ; 0.879 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 894 ; 4.912 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 328 ;34.430 ;24.177 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1222 ;11.832 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;15.017 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1100 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8249 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1699 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6PYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57664 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 97.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.320 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NOT AVAILABLE, VAPOR DIFFUSION, REMARK 280 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 29.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.85950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.95700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.85950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.95700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 PRO A 200 REMARK 465 ASN A 201 REMARK 465 ASN A 202 REMARK 465 LEU A 233 REMARK 465 LEU A 234 REMARK 465 SER A 235 REMARK 465 SER A 236 REMARK 465 GLU A 237 REMARK 465 GLN A 238 REMARK 465 LEU A 239 REMARK 465 LYS A 240 REMARK 465 LEU A 241 REMARK 465 CYS A 242 REMARK 465 VAL A 243 REMARK 465 LEU A 244 REMARK 465 GLU A 245 REMARK 465 ARG A 310 REMARK 465 ILE A 311 REMARK 465 SER A 312 REMARK 465 THR A 313 REMARK 465 ALA A 314 REMARK 465 THR A 315 REMARK 465 PRO A 316 REMARK 465 TYR A 317 REMARK 465 MET A 318 REMARK 465 ASN A 319 REMARK 465 GLY A 320 REMARK 465 GLU A 321 REMARK 465 ILE A 348 REMARK 465 ARG A 349 REMARK 465 ASP A 350 REMARK 465 LYS A 410 REMARK 465 GLY A 411 REMARK 465 ARG A 412 REMARK 465 LYS A 413 REMARK 465 GLY A 414 REMARK 465 ALA A 415 REMARK 465 LYS A 416 REMARK 465 GLY A 864 REMARK 465 GLY A 865 REMARK 465 LEU A 866 REMARK 465 LYS A 867 REMARK 465 GLY A 868 REMARK 465 ALA A 869 REMARK 465 LEU A 870 REMARK 465 GLN A 871 REMARK 465 PHE A 872 REMARK 465 LYS A 941 REMARK 465 LYS A 942 REMARK 465 LYS A 943 REMARK 465 LYS A 944 REMARK 465 PHE A 945 REMARK 465 GLY A 946 REMARK 465 TYR A 947 REMARK 465 LYS A 948 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 GLU A 109 CD OE1 OE2 REMARK 480 LYS A 111 CD CE NZ REMARK 480 MET A 130 CE REMARK 480 LYS A 132 CE NZ REMARK 480 GLU A 176 CG CD OE1 OE2 REMARK 480 LEU A 177 CG CD1 CD2 REMARK 480 LYS A 179 CG CD CE NZ REMARK 480 ILE A 181 CG1 CG2 CD1 REMARK 480 ASN A 183 CG OD1 ND2 REMARK 480 LYS A 184 CG CD CE NZ REMARK 480 LYS A 187 CG CD CE NZ REMARK 480 ILE A 194 CD1 REMARK 480 ILE A 197 CD1 REMARK 480 LYS A 204 CD CE NZ REMARK 480 ASP A 214 CG OD1 OD2 REMARK 480 GLU A 223 CG CD OE1 OE2 REMARK 480 ILE A 225 CG1 CG2 CD1 REMARK 480 ARG A 226 NE CZ NH1 NH2 REMARK 480 ARG A 230 NE CZ NH1 NH2 REMARK 480 TYR A 246 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 GLN A 247 CD OE1 NE2 REMARK 480 LYS A 249 CG CD CE NZ REMARK 480 LYS A 264 CG CD CE NZ REMARK 480 MET A 278 CG SD CE REMARK 480 ARG A 281 NE CZ NH1 NH2 REMARK 480 LYS A 290 CE NZ REMARK 480 GLU A 291 CG CD OE1 OE2 REMARK 480 GLN A 296 CG CD OE1 NE2 REMARK 480 MET A 299 CG SD CE REMARK 480 CYS A 301 SG REMARK 480 ARG A 309 CD NE CZ NH1 NH2 REMARK 480 LYS A 325 CG CD CE NZ REMARK 480 ASN A 331 CG OD1 ND2 REMARK 480 LYS A 337 CE NZ REMARK 480 ASN A 347 CG OD1 ND2 REMARK 480 ASP A 352 CG OD1 OD2 REMARK 480 LYS A 353 CD CE NZ REMARK 480 GLN A 374 CD OE1 NE2 REMARK 480 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 418 CG CD OE1 OE2 REMARK 480 ILE A 427 CD1 REMARK 480 LYS A 440 CD CE NZ REMARK 480 HIS A 450 CG ND1 CD2 CE1 NE2 REMARK 480 GLU A 453 CG CD OE1 OE2 REMARK 480 SER A 481 OG REMARK 480 LYS A 485 NZ REMARK 480 ASN A 497 CG OD1 ND2 REMARK 480 ARG A 502 CD NE CZ NH1 NH2 REMARK 480 ASP A 520 CG OD1 OD2 REMARK 480 ASN A 521 CG OD1 ND2 REMARK 480 GLU A 522 CD OE1 OE2 REMARK 480 LEU A 523 CG CD1 CD2 REMARK 480 ARG A 524 CD NE CZ NH1 NH2 REMARK 480 GLU A 525 CG CD OE1 OE2 REMARK 480 ASN A 526 CG OD1 ND2 REMARK 480 LYS A 528 CE NZ REMARK 480 LYS A 532 CD CE NZ REMARK 480 GLU A 542 CG CD OE1 OE2 REMARK 480 GLN A 546 CD OE1 NE2 REMARK 480 LYS A 588 CE NZ REMARK 480 LYS A 594 CE NZ REMARK 480 LYS A 621 CE NZ REMARK 480 LYS A 655 NZ REMARK 480 GLN A 721 CG CD OE1 NE2 REMARK 480 LYS A 723 NZ REMARK 480 LYS A 724 CD CE NZ REMARK 480 LYS A 729 NZ REMARK 480 LYS A 733 CG CD CE NZ REMARK 480 ARG A 852 CD NE CZ NH1 NH2 REMARK 480 GLN A 861 CG CD OE1 NE2 REMARK 480 LYS A 863 NZ REMARK 480 LYS A 882 CE NZ REMARK 480 GLU A 888 CG CD OE1 OE2 REMARK 480 ILE A 913 CD1 REMARK 480 ARG A 949 CD NE CZ NH1 NH2 REMARK 480 GLN A 969 CG CD OE1 NE2 REMARK 480 GLU A 970 CG CD OE1 OE2 REMARK 480 LYS A 973 CE NZ REMARK 480 ARG A 975 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 982 CD OE1 OE2 REMARK 480 LYS A 986 CE NZ REMARK 480 GLU A 1012 CD OE1 OE2 REMARK 480 ILE A 1022 CD1 REMARK 480 LYS A 1024 CG CD CE NZ REMARK 480 LYS A 1030 NZ REMARK 480 GLU A 1037 CG CD OE1 OE2 REMARK 480 LYS A 1041 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 ASP A 352 CB ASP A 352 CG -0.139 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 PHE A 261 72.16 -107.73 REMARK 500 ASP A 352 -118.76 -72.30 REMARK 500 CYS A 378 -17.84 92.02 REMARK 500 TRP A 383 -61.61 -138.27 REMARK 500 GLU A 469 55.35 -95.15 REMARK 500 ASN A 756 104.14 -160.04 REMARK 500 LYS A 776 -10.72 73.44 REMARK 500 ARG A 777 67.48 61.44 REMARK 500 LEU A 793 -66.50 -121.93 REMARK 500 ASP A 933 81.46 60.06 REMARK 500 LEU A 938 -152.07 59.23 REMARK 500 LEU A 956 95.75 -59.82 REMARK 500 LYS A 973 75.93 -105.92 REMARK 500 HIS A1048 63.84 60.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 GOL A 1103 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P5J A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1103 DBREF 6PYS A 107 1051 UNP P42336 PK3CA_HUMAN 107 1051 SEQRES 1 A 945 ASN ARG GLU GLU LYS ILE LEU ASN ARG GLU ILE GLY PHE SEQRES 2 A 945 ALA ILE GLY MET PRO VAL CYS GLU PHE ASP MET VAL LYS SEQRES 3 A 945 ASP PRO GLU VAL GLN ASP PHE ARG ARG ASN ILE LEU ASN SEQRES 4 A 945 VAL CYS LYS GLU ALA VAL ASP LEU ARG ASP LEU ASN SER SEQRES 5 A 945 PRO HIS SER ARG ALA MET TYR VAL TYR PRO PRO ASN VAL SEQRES 6 A 945 GLU SER SER PRO GLU LEU PRO LYS HIS ILE TYR ASN LYS SEQRES 7 A 945 LEU ASP LYS GLY GLN ILE ILE VAL VAL ILE TRP VAL ILE SEQRES 8 A 945 VAL SER PRO ASN ASN ASP LYS GLN LYS TYR THR LEU LYS SEQRES 9 A 945 ILE ASN HIS ASP CYS VAL PRO GLU GLN VAL ILE ALA GLU SEQRES 10 A 945 ALA ILE ARG LYS LYS THR ARG SER MET LEU LEU SER SER SEQRES 11 A 945 GLU GLN LEU LYS LEU CYS VAL LEU GLU TYR GLN GLY LYS SEQRES 12 A 945 TYR ILE LEU LYS VAL CYS GLY CYS ASP GLU TYR PHE LEU SEQRES 13 A 945 GLU LYS TYR PRO LEU SER GLN TYR LYS TYR ILE ARG SER SEQRES 14 A 945 CYS ILE MET LEU GLY ARG MET PRO ASN LEU MET LEU MET SEQRES 15 A 945 ALA LYS GLU SER LEU TYR SER GLN LEU PRO MET ASP CYS SEQRES 16 A 945 PHE THR MET PRO SER TYR SER ARG ARG ILE SER THR ALA SEQRES 17 A 945 THR PRO TYR MET ASN GLY GLU THR SER THR LYS SER LEU SEQRES 18 A 945 TRP VAL ILE ASN SER ALA LEU ARG ILE LYS ILE LEU CYS SEQRES 19 A 945 ALA THR TYR VAL ASN VAL ASN ILE ARG ASP ILE ASP LYS SEQRES 20 A 945 ILE TYR VAL ARG THR GLY ILE TYR HIS GLY GLY GLU PRO SEQRES 21 A 945 LEU CYS ASP ASN VAL ASN THR GLN ARG VAL PRO CYS SER SEQRES 22 A 945 ASN PRO ARG TRP ASN GLU TRP LEU ASN TYR ASP ILE TYR SEQRES 23 A 945 ILE PRO ASP LEU PRO ARG ALA ALA ARG LEU CYS LEU SER SEQRES 24 A 945 ILE CYS SER VAL LYS GLY ARG LYS GLY ALA LYS GLU GLU SEQRES 25 A 945 HIS CYS PRO LEU ALA TRP GLY ASN ILE ASN LEU PHE ASP SEQRES 26 A 945 TYR THR ASP THR LEU VAL SER GLY LYS MET ALA LEU ASN SEQRES 27 A 945 LEU TRP PRO VAL PRO HIS GLY LEU GLU ASP LEU LEU ASN SEQRES 28 A 945 PRO ILE GLY VAL THR GLY SER ASN PRO ASN LYS GLU THR SEQRES 29 A 945 PRO CYS LEU GLU LEU GLU PHE ASP TRP PHE SER SER VAL SEQRES 30 A 945 VAL LYS PHE PRO ASP MET SER VAL ILE GLU GLU HIS ALA SEQRES 31 A 945 ASN TRP SER VAL SER ARG GLU ALA GLY PHE SER TYR SER SEQRES 32 A 945 HIS ALA GLY LEU SER ASN ARG LEU ALA ARG ASP ASN GLU SEQRES 33 A 945 LEU ARG GLU ASN ASP LYS GLU GLN LEU LYS ALA ILE SER SEQRES 34 A 945 THR ARG ASP PRO LEU SER GLU ILE THR GLU GLN GLU LYS SEQRES 35 A 945 ASP PHE LEU TRP SER HIS ARG HIS TYR CYS VAL THR ILE SEQRES 36 A 945 PRO GLU ILE LEU PRO LYS LEU LEU LEU SER VAL LYS TRP SEQRES 37 A 945 ASN SER ARG ASP GLU VAL ALA GLN MET TYR CYS LEU VAL SEQRES 38 A 945 LYS ASP TRP PRO PRO ILE LYS PRO GLU GLN ALA MET GLU SEQRES 39 A 945 LEU LEU ASP CYS ASN TYR PRO ASP PRO MET VAL ARG GLY SEQRES 40 A 945 PHE ALA VAL ARG CYS LEU GLU LYS TYR LEU THR ASP ASP SEQRES 41 A 945 LYS LEU SER GLN TYR LEU ILE GLN LEU VAL GLN VAL LEU SEQRES 42 A 945 LYS TYR GLU GLN TYR LEU ASP ASN LEU LEU VAL ARG PHE SEQRES 43 A 945 LEU LEU LYS LYS ALA LEU THR ASN GLN ARG ILE GLY HIS SEQRES 44 A 945 PHE PHE PHE TRP HIS LEU LYS SER GLU MET HIS ASN LYS SEQRES 45 A 945 THR VAL SER GLN ARG PHE GLY LEU LEU LEU GLU SER TYR SEQRES 46 A 945 CYS ARG ALA CYS GLY MET TYR LEU LYS HIS LEU ASN ARG SEQRES 47 A 945 GLN VAL GLU ALA MET GLU LYS LEU ILE ASN LEU THR ASP SEQRES 48 A 945 ILE LEU LYS GLN GLU LYS LYS ASP GLU THR GLN LYS VAL SEQRES 49 A 945 GLN MET LYS PHE LEU VAL GLU GLN MET ARG ARG PRO ASP SEQRES 50 A 945 PHE MET ASP ALA LEU GLN GLY PHE LEU SER PRO LEU ASN SEQRES 51 A 945 PRO ALA HIS GLN LEU GLY ASN LEU ARG LEU GLU GLU CYS SEQRES 52 A 945 ARG ILE MET SER SER ALA LYS ARG PRO LEU TRP LEU ASN SEQRES 53 A 945 TRP GLU ASN PRO ASP ILE MET SER GLU LEU LEU PHE GLN SEQRES 54 A 945 ASN ASN GLU ILE ILE PHE LYS ASN GLY ASP ASP LEU ARG SEQRES 55 A 945 GLN ASP MET LEU THR LEU GLN ILE ILE ARG ILE MET GLU SEQRES 56 A 945 ASN ILE TRP GLN ASN GLN GLY LEU ASP LEU ARG MET LEU SEQRES 57 A 945 PRO TYR GLY CYS LEU SER ILE GLY ASP CYS VAL GLY LEU SEQRES 58 A 945 ILE GLU VAL VAL ARG ASN SER HIS THR ILE MET GLN ILE SEQRES 59 A 945 GLN CYS LYS GLY GLY LEU LYS GLY ALA LEU GLN PHE ASN SEQRES 60 A 945 SER HIS THR LEU HIS GLN TRP LEU LYS ASP LYS ASN LYS SEQRES 61 A 945 GLY GLU ILE TYR ASP ALA ALA ILE ASP LEU PHE THR ARG SEQRES 62 A 945 SER CYS ALA GLY TYR CYS VAL ALA THR PHE ILE LEU GLY SEQRES 63 A 945 ILE GLY ASP ARG HIS ASN SER ASN ILE MET VAL LYS ASP SEQRES 64 A 945 ASP GLY GLN LEU PHE HIS ILE ASP PHE GLY HIS PHE LEU SEQRES 65 A 945 ASP HIS LYS LYS LYS LYS PHE GLY TYR LYS ARG GLU ARG SEQRES 66 A 945 VAL PRO PHE VAL LEU THR GLN ASP PHE LEU ILE VAL ILE SEQRES 67 A 945 SER LYS GLY ALA GLN GLU CYS THR LYS THR ARG GLU PHE SEQRES 68 A 945 GLU ARG PHE GLN GLU MET CYS TYR LYS ALA TYR LEU ALA SEQRES 69 A 945 ILE ARG GLN HIS ALA ASN LEU PHE ILE ASN LEU PHE SER SEQRES 70 A 945 MET MET LEU GLY SER GLY MET PRO GLU LEU GLN SER PHE SEQRES 71 A 945 ASP ASP ILE ALA TYR ILE ARG LYS THR LEU ALA LEU ASP SEQRES 72 A 945 LYS THR GLU GLN GLU ALA LEU GLU TYR PHE MET LYS GLN SEQRES 73 A 945 MET ASN ASP ALA HIS HIS GLY GLY TRP HET P5J A1101 34 HET GOL A1102 6 HET GOL A1103 6 HETNAM P5J (3S)-3-BENZYL-3-METHYL-5-[5-(2-METHYLPYRIMIDIN-5-YL) HETNAM 2 P5J PYRAZOLO[1,5-A]PYRIMIDIN-3-YL]-1,3-DIHYDRO-2H-INDOL-2- HETNAM 3 P5J ONE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 P5J C27 H22 N6 O FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *162(H2 O) HELIX 1 AA1 ASN A 107 GLY A 122 1 16 HELIX 2 AA2 VAL A 125 MET A 130 1 6 HELIX 3 AA3 ASP A 133 ASP A 155 1 23 HELIX 4 AA4 PRO A 159 TYR A 167 1 9 HELIX 5 AA5 PRO A 178 ASN A 183 1 6 HELIX 6 AA6 VAL A 216 SER A 231 1 16 HELIX 7 AA7 PRO A 266 GLN A 269 5 4 HELIX 8 AA8 TYR A 270 GLY A 280 1 11 HELIX 9 AA9 LYS A 290 LEU A 297 1 8 HELIX 10 AB1 PRO A 305 ARG A 309 5 5 HELIX 11 AB2 TRP A 328 ILE A 330 5 3 HELIX 12 AB3 PRO A 394 LEU A 396 5 3 HELIX 13 AB4 ASP A 488 GLY A 505 1 18 HELIX 14 AB5 SER A 507 GLY A 512 1 6 HELIX 15 AB6 ARG A 519 LEU A 523 5 5 HELIX 16 AB7 ARG A 524 THR A 536 1 13 HELIX 17 AB8 THR A 544 HIS A 554 1 11 HELIX 18 AB9 HIS A 556 GLU A 563 5 8 HELIX 19 AC1 ILE A 564 VAL A 572 1 9 HELIX 20 AC2 SER A 576 ASP A 589 1 14 HELIX 21 AC3 LYS A 594 LEU A 601 1 8 HELIX 22 AC4 ASP A 608 LEU A 623 1 16 HELIX 23 AC5 THR A 624 TYR A 631 1 8 HELIX 24 AC6 TYR A 631 VAL A 638 1 8 HELIX 25 AC7 LEU A 639 GLU A 642 5 4 HELIX 26 AC8 ASN A 647 ASN A 660 1 14 HELIX 27 AC9 ASN A 660 SER A 673 1 14 HELIX 28 AD1 VAL A 680 CYS A 695 1 16 HELIX 29 AD2 MET A 697 GLU A 722 1 26 HELIX 30 AD3 THR A 727 ARG A 740 1 14 HELIX 31 AD4 ARG A 741 LEU A 748 1 8 HELIX 32 AD5 MET A 789 LEU A 793 5 5 HELIX 33 AD6 LEU A 807 GLN A 827 1 21 HELIX 34 AD7 ILE A 857 CYS A 862 1 6 HELIX 35 AD8 HIS A 875 ASN A 885 1 11 HELIX 36 AD9 LYS A 886 GLU A 888 5 3 HELIX 37 AE1 ILE A 889 GLY A 912 1 24 HELIX 38 AE2 THR A 957 SER A 965 1 9 HELIX 39 AE3 THR A 974 GLN A 993 1 20 HELIX 40 AE4 HIS A 994 MET A 1004 1 11 HELIX 41 AE5 SER A 1015 LEU A 1026 1 12 HELIX 42 AE6 THR A 1031 HIS A 1048 1 18 SHEET 1 AA1 4 LYS A 204 ASN A 212 0 SHEET 2 AA1 4 GLN A 189 ILE A 197 -1 N VAL A 192 O LEU A 209 SHEET 3 AA1 4 ASN A 284 ALA A 289 1 O LEU A 285 N TRP A 195 SHEET 4 AA1 4 TYR A 250 VAL A 254 -1 N LYS A 253 O MET A 286 SHEET 1 AA2 2 SER A 323 SER A 326 0 SHEET 2 AA2 2 SER A 482 LYS A 485 1 O VAL A 483 N SER A 323 SHEET 1 AA3 4 ARG A 382 TYR A 392 0 SHEET 2 AA3 4 ALA A 333 THR A 342 -1 N LEU A 339 O TRP A 383 SHEET 3 AA3 4 CYS A 472 PHE A 477 -1 O GLU A 474 N CYS A 340 SHEET 4 AA3 4 GLY A 439 ASN A 444 -1 N MET A 441 O LEU A 475 SHEET 1 AA4 3 GLU A 365 PRO A 366 0 SHEET 2 AA4 3 ILE A 354 HIS A 362 -1 N HIS A 362 O GLU A 365 SHEET 3 AA4 3 VAL A 371 ASN A 372 -1 O VAL A 371 N THR A 358 SHEET 1 AA5 5 GLU A 365 PRO A 366 0 SHEET 2 AA5 5 ILE A 354 HIS A 362 -1 N HIS A 362 O GLU A 365 SHEET 3 AA5 5 ARG A 401 SER A 408 -1 O CYS A 403 N GLY A 359 SHEET 4 AA5 5 CYS A 420 ASN A 428 -1 O LEU A 422 N ILE A 406 SHEET 5 AA5 5 TRP A 446 PRO A 447 -1 O TRP A 446 N TRP A 424 SHEET 1 AA6 2 PHE A 751 LEU A 752 0 SHEET 2 AA6 2 GLN A 760 LEU A 761 -1 O LEU A 761 N PHE A 751 SHEET 1 AA7 5 ARG A 770 ILE A 771 0 SHEET 2 AA7 5 LEU A 779 GLU A 784 -1 O TRP A 780 N ARG A 770 SHEET 3 AA7 5 ASN A 796 ASN A 803 -1 O PHE A 801 N LEU A 779 SHEET 4 AA7 5 VAL A 845 GLU A 849 -1 O ILE A 848 N ILE A 800 SHEET 5 AA7 5 CYS A 838 GLY A 842 -1 N LEU A 839 O LEU A 847 SHEET 1 AA8 3 SER A 854 THR A 856 0 SHEET 2 AA8 3 ILE A 921 LYS A 924 -1 O VAL A 923 N HIS A 855 SHEET 3 AA8 3 LEU A 929 HIS A 931 -1 O PHE A 930 N MET A 922 CISPEP 1 SER A 158 PRO A 159 0 1.56 SITE 1 AC1 11 SER A 774 LYS A 802 TYR A 836 ILE A 848 SITE 2 AC1 11 GLU A 849 VAL A 850 VAL A 851 SER A 854 SITE 3 AC1 11 THR A 856 GLN A 859 MET A 922 SITE 1 AC2 5 GLU A 503 ARG A 516 TRP A 552 GLU A 579 SITE 2 AC2 5 HOH A1237 SITE 1 AC3 3 VAL A 572 TRP A 574 ASN A 575 CRYST1 58.440 133.914 141.719 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 0.017112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007467 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007056 0.00000