HEADER TRANSFERASE 02-JUN-08 3DBS TITLE STRUCTURE OF PI3K GAMMA IN COMPLEX WITH GDC0941 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC COMPND 3 SUBUNIT GAMMA ISOFORM; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PI3K GAMMA, UNP RESIDUES 143-1102; COMPND 6 SYNONYM: PI3-KINASE P110 SUBUNIT GAMMA, PTDINS-3-KINASE SUBUNIT P110, COMPND 7 PI3K, PI3KGAMMA, P120-PI3K; COMPND 8 EC: 2.7.1.153 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS PI3K GAMMA, INHIBITOR, KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.WIESMANN,M.ULTSCH REVDAT 5 01-NOV-23 3DBS 1 REMARK SEQADV REVDAT 4 13-JUL-11 3DBS 1 VERSN REVDAT 3 24-FEB-09 3DBS 1 VERSN REVDAT 2 07-OCT-08 3DBS 1 JRNL REVDAT 1 17-JUN-08 3DBS 0 JRNL AUTH A.J.FOLKES,K.AHMADI,W.K.ALDERTON,S.ALIX,S.J.BAKER,G.BOX, JRNL AUTH 2 I.S.CHUCKOWREE,P.A.CLARKE,P.DEPLEDGE,S.A.ECCLES, JRNL AUTH 3 L.S.FRIEDMAN,A.HAYES,T.C.HANCOX,A.KUGENDRADAS,L.LENSUN, JRNL AUTH 4 P.MOORE,A.G.OLIVERO,J.PANG,S.PATEL,G.H.PERGL-WILSON, JRNL AUTH 5 F.I.RAYNAUD,A.ROBSON,N.SAGHIR,L.SALPHATI,S.SOHAL,M.H.ULTSCH, JRNL AUTH 6 M.VALENTI,H.J.A.WALLWEBER,N.C.WAN,C.WIESMANN,P.WORKMAN, JRNL AUTH 7 A.ZHYVOLOUP,M.J.ZVELEBIL,S.J.SHUTTLEWORTH JRNL TITL THE IDENTIFICATION OF JRNL TITL 2 2-(1H-INDAZOL-4-YL) JRNL TITL 3 -6-(4-METHANESULFONYL-PIPERAZIN-1-YLMETHYL) JRNL TITL 4 -4-MORPHOLIN-4-YL-THIENO[3,2-D]PYRIMIDINE (GDC-0941) AS A JRNL TITL 5 POTENT, SELECTIVE, ORALLY BIOAVAILABLE INHIBITOR OF CLASS I JRNL TITL 6 PI3 KINASE FOR THE TREATMENT OF CANCER JRNL REF J.MED.CHEM. V. 51 5522 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18754654 JRNL DOI 10.1021/JM800295D REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24173 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1314 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1404 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6812 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -2.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.397 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.343 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.311 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6998 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 6398 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9471 ; 1.302 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14912 ; 0.847 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 833 ; 6.588 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1060 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7597 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1393 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1982 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 7369 ; 0.211 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 5077 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 90 ; 0.170 ; 0.200 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): 13 ; 0.143 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 33 ; 0.205 ; 0.200 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): 4195 ; 2.473 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6804 ; 3.915 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2803 ; 2.552 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2667 ; 4.047 ; 5.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 143 A 1091 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8171 47.3052 27.3877 REMARK 3 T TENSOR REMARK 3 T11: 0.3440 T22: 0.0297 REMARK 3 T33: 0.1974 T12: 0.0761 REMARK 3 T13: 0.0732 T23: 0.0646 REMARK 3 L TENSOR REMARK 3 L11: 5.0801 L22: 1.5389 REMARK 3 L33: 2.9445 L12: -1.0755 REMARK 3 L13: 0.6680 L23: -0.3765 REMARK 3 S TENSOR REMARK 3 S11: 0.0155 S12: 0.0520 S13: -0.1592 REMARK 3 S21: 0.1806 S22: 0.1947 S23: 0.3480 REMARK 3 S31: -0.5801 S32: -0.2581 S33: -0.2102 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3DBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1E8Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, LI2SO4, PH 7.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 72.14200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.88100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.14200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.88100 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 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 LYS A 254 REMARK 465 LYS A 255 REMARK 465 LYS A 256 REMARK 465 SER A 257 REMARK 465 LEU A 258 REMARK 465 MET A 259 REMARK 465 ASP A 260 REMARK 465 ILE A 261 REMARK 465 PRO A 262 REMARK 465 GLU A 263 REMARK 465 SER A 264 REMARK 465 GLN A 265 REMARK 465 SER A 266 REMARK 465 TRP A 323 REMARK 465 PRO A 324 REMARK 465 LEU A 325 REMARK 465 VAL A 326 REMARK 465 ASP A 327 REMARK 465 ASP A 328 REMARK 465 CYS A 329 REMARK 465 THR A 330 REMARK 465 GLY A 331 REMARK 465 VAL A 332 REMARK 465 THR A 333 REMARK 465 GLY A 334 REMARK 465 TYR A 335 REMARK 465 HIS A 336 REMARK 465 GLU A 337 REMARK 465 GLN A 338 REMARK 465 LEU A 339 REMARK 465 THR A 340 REMARK 465 ILE A 341 REMARK 465 HIS A 342 REMARK 465 GLY A 343 REMARK 465 LYS A 344 REMARK 465 ASP A 345 REMARK 465 HIS A 346 REMARK 465 GLU A 347 REMARK 465 SER A 348 REMARK 465 VAL A 349 REMARK 465 PHE A 350 REMARK 465 THR A 351 REMARK 465 VAL A 352 REMARK 465 SER A 353 REMARK 465 LEU A 354 REMARK 465 TRP A 355 REMARK 465 ASP A 356 REMARK 465 GLY A 436 REMARK 465 LYS A 437 REMARK 465 ALA A 438 REMARK 465 PRO A 439 REMARK 465 ALA A 440 REMARK 465 LEU A 441 REMARK 465 SER A 442 REMARK 465 SER A 443 REMARK 465 LYS A 444 REMARK 465 ALA A 445 REMARK 465 SER A 446 REMARK 465 ALA A 447 REMARK 465 GLU A 448 REMARK 465 SER A 449 REMARK 465 PRO A 450 REMARK 465 SER A 451 REMARK 465 SER A 452 REMARK 465 GLU A 453 REMARK 465 SER A 454 REMARK 465 LYS A 455 REMARK 465 GLY A 456 REMARK 465 LYS A 457 REMARK 465 VAL A 458 REMARK 465 GLN A 459 REMARK 465 LYS A 490 REMARK 465 GLY A 491 REMARK 465 GLU A 492 REMARK 465 ASP A 493 REMARK 465 GLN A 494 REMARK 465 GLY A 495 REMARK 465 SER A 496 REMARK 465 TYR A 523 REMARK 465 CYS A 524 REMARK 465 LEU A 529 REMARK 465 PRO A 530 REMARK 465 LYS A 531 REMARK 465 HIS A 532 REMARK 465 GLN A 533 REMARK 465 PRO A 534 REMARK 465 THR A 535 REMARK 465 PRO A 536 REMARK 465 ASP A 537 REMARK 465 PRO A 538 REMARK 465 GLU A 539 REMARK 465 GLY A 540 REMARK 465 ASP A 541 REMARK 465 ARG A 542 REMARK 465 VAL A 543 REMARK 465 ILE A 968 REMARK 465 LEU A 969 REMARK 465 GLY A 970 REMARK 465 ASN A 971 REMARK 465 TYR A 972 REMARK 465 LYS A 973 REMARK 465 SER A 974 REMARK 465 PHE A 975 REMARK 465 LEU A 976 REMARK 465 GLY A 977 REMARK 465 ILE A 978 REMARK 465 ASN A 979 REMARK 465 LYS A 980 REMARK 465 LEU A 1092 REMARK 465 GLY A 1093 REMARK 465 ILE A 1094 REMARK 465 LYS A 1095 REMARK 465 GLN A 1096 REMARK 465 GLY A 1097 REMARK 465 GLU A 1098 REMARK 465 LYS A 1099 REMARK 465 HIS A 1100 REMARK 465 SER A 1101 REMARK 465 ALA A 1102 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 MET A 143 CG SD CE REMARK 470 GLU A 322 CB CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 802 O1 GD9 A 1 2.14 REMARK 500 OG SER A 204 OE2 GLU A 652 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 904 CG ASP A 904 OD1 0.174 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 278 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 378 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 632 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 837 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 874 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A1011 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A1070 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES 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 ASN A 217 0.51 -154.69 REMARK 500 ARG A 226 105.92 -160.00 REMARK 500 SER A 227 -96.71 39.44 REMARK 500 THR A 228 -88.36 -74.88 REMARK 500 SER A 230 106.68 -172.46 REMARK 500 PHE A 248 -54.73 -125.55 REMARK 500 MET A 252 -43.52 -171.46 REMARK 500 ASP A 278 66.34 -112.97 REMARK 500 PRO A 374 133.85 -31.67 REMARK 500 ARG A 375 -72.96 -124.47 REMARK 500 ASN A 376 -46.19 -168.49 REMARK 500 LEU A 379 -163.56 -125.73 REMARK 500 ASP A 509 85.67 -65.40 REMARK 500 ILE A 527 71.41 30.84 REMARK 500 ALA A 545 138.69 65.80 REMARK 500 ARG A 613 78.45 -105.32 REMARK 500 LYS A 756 104.07 -162.33 REMARK 500 TYR A 757 118.80 -163.58 REMARK 500 ASP A 758 -146.31 65.06 REMARK 500 ASN A 776 -100.62 -67.27 REMARK 500 GLN A 778 -61.03 -169.95 REMARK 500 ALA A 805 72.66 -61.26 REMARK 500 LYS A 808 31.62 74.18 REMARK 500 CYS A 869 114.95 -172.85 REMARK 500 VAL A 896 -72.73 12.11 REMARK 500 ASN A 898 85.92 -49.25 REMARK 500 THR A 899 22.51 42.90 REMARK 500 ASN A 951 32.55 -93.37 REMARK 500 LEU A 987 59.91 -148.90 REMARK 500 SER A 998 59.09 -96.85 REMARK 500 HIS A1022 6.61 -68.54 REMARK 500 HIS A1023 32.57 -141.91 REMARK 500 PRO A1040 -162.51 -55.64 REMARK 500 THR A1043 98.68 -66.04 REMARK 500 SER A1044 -8.15 -53.82 REMARK 500 GLU A1049 -3.20 -59.62 REMARK 500 TRP A1086 99.79 -68.52 REMARK 500 PHE A1087 -48.67 150.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 756 TYR A 757 142.71 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 GD9 A 1 DBREF 3DBS A 144 1102 UNP P48736 PK3CG_HUMAN 144 1102 SEQADV 3DBS MET A 143 UNP P48736 INITIATING METHIONINE SEQRES 1 A 960 MET SER GLU GLU SER GLN ALA PHE GLN ARG GLN LEU THR SEQRES 2 A 960 ALA LEU ILE GLY TYR ASP VAL THR ASP VAL SER ASN VAL SEQRES 3 A 960 HIS ASP ASP GLU LEU GLU PHE THR ARG ARG GLY LEU VAL SEQRES 4 A 960 THR PRO ARG MET ALA GLU VAL ALA SER ARG ASP PRO LYS SEQRES 5 A 960 LEU TYR ALA MET HIS PRO TRP VAL THR SER LYS PRO LEU SEQRES 6 A 960 PRO GLU TYR LEU TRP LYS LYS ILE ALA ASN ASN CYS ILE SEQRES 7 A 960 PHE ILE VAL ILE HIS ARG SER THR THR SER GLN THR ILE SEQRES 8 A 960 LYS VAL SER PRO ASP ASP THR PRO GLY ALA ILE LEU GLN SEQRES 9 A 960 SER PHE PHE THR LYS MET ALA LYS LYS LYS SER LEU MET SEQRES 10 A 960 ASP ILE PRO GLU SER GLN SER GLU GLN ASP PHE VAL LEU SEQRES 11 A 960 ARG VAL CYS GLY ARG ASP GLU TYR LEU VAL GLY GLU THR SEQRES 12 A 960 PRO ILE LYS ASN PHE GLN TRP VAL ARG HIS CYS LEU LYS SEQRES 13 A 960 ASN GLY GLU GLU ILE HIS VAL VAL LEU ASP THR PRO PRO SEQRES 14 A 960 ASP PRO ALA LEU ASP GLU VAL ARG LYS GLU GLU TRP PRO SEQRES 15 A 960 LEU VAL ASP ASP CYS THR GLY VAL THR GLY TYR HIS GLU SEQRES 16 A 960 GLN LEU THR ILE HIS GLY LYS ASP HIS GLU SER VAL PHE SEQRES 17 A 960 THR VAL SER LEU TRP ASP CYS ASP ARG LYS PHE ARG VAL SEQRES 18 A 960 LYS ILE ARG GLY ILE ASP ILE PRO VAL LEU PRO ARG ASN SEQRES 19 A 960 THR ASP LEU THR VAL PHE VAL GLU ALA ASN ILE GLN HIS SEQRES 20 A 960 GLY GLN GLN VAL LEU CYS GLN ARG ARG THR SER PRO LYS SEQRES 21 A 960 PRO PHE THR GLU GLU VAL LEU TRP ASN VAL TRP LEU GLU SEQRES 22 A 960 PHE SER ILE LYS ILE LYS ASP LEU PRO LYS GLY ALA LEU SEQRES 23 A 960 LEU ASN LEU GLN ILE TYR CYS GLY LYS ALA PRO ALA LEU SEQRES 24 A 960 SER SER LYS ALA SER ALA GLU SER PRO SER SER GLU SER SEQRES 25 A 960 LYS GLY LYS VAL GLN LEU LEU TYR TYR VAL ASN LEU LEU SEQRES 26 A 960 LEU ILE ASP HIS ARG PHE LEU LEU ARG ARG GLY GLU TYR SEQRES 27 A 960 VAL LEU HIS MET TRP GLN ILE SER GLY LYS GLY GLU ASP SEQRES 28 A 960 GLN GLY SER PHE ASN ALA ASP LYS LEU THR SER ALA THR SEQRES 29 A 960 ASN PRO ASP LYS GLU ASN SER MET SER ILE SER ILE LEU SEQRES 30 A 960 LEU ASP ASN TYR CYS HIS PRO ILE ALA LEU PRO LYS HIS SEQRES 31 A 960 GLN PRO THR PRO ASP PRO GLU GLY ASP ARG VAL ARG ALA SEQRES 32 A 960 GLU MET PRO ASN GLN LEU ARG LYS GLN LEU GLU ALA ILE SEQRES 33 A 960 ILE ALA THR ASP PRO LEU ASN PRO LEU THR ALA GLU ASP SEQRES 34 A 960 LYS GLU LEU LEU TRP HIS PHE ARG TYR GLU SER LEU LYS SEQRES 35 A 960 HIS PRO LYS ALA TYR PRO LYS LEU PHE SER SER VAL LYS SEQRES 36 A 960 TRP GLY GLN GLN GLU ILE VAL ALA LYS THR TYR GLN LEU SEQRES 37 A 960 LEU ALA ARG ARG GLU VAL TRP ASP GLN SER ALA LEU ASP SEQRES 38 A 960 VAL GLY LEU THR MET GLN LEU LEU ASP CYS ASN PHE SER SEQRES 39 A 960 ASP GLU ASN VAL ARG ALA ILE ALA VAL GLN LYS LEU GLU SEQRES 40 A 960 SER LEU GLU ASP ASP ASP VAL LEU HIS TYR LEU LEU GLN SEQRES 41 A 960 LEU VAL GLN ALA VAL LYS PHE GLU PRO TYR HIS ASP SER SEQRES 42 A 960 ALA LEU ALA ARG PHE LEU LEU LYS ARG GLY LEU ARG ASN SEQRES 43 A 960 LYS ARG ILE GLY HIS PHE LEU PHE TRP PHE LEU ARG SER SEQRES 44 A 960 GLU ILE ALA GLN SER ARG HIS TYR GLN GLN ARG PHE ALA SEQRES 45 A 960 VAL ILE LEU GLU ALA TYR LEU ARG GLY CYS GLY THR ALA SEQRES 46 A 960 MET LEU HIS ASP PHE THR GLN GLN VAL GLN VAL ILE GLU SEQRES 47 A 960 MET LEU GLN LYS VAL THR LEU ASP ILE LYS SER LEU SER SEQRES 48 A 960 ALA GLU LYS TYR ASP VAL SER SER GLN VAL ILE SER GLN SEQRES 49 A 960 LEU LYS GLN LYS LEU GLU ASN LEU GLN ASN SER GLN LEU SEQRES 50 A 960 PRO GLU SER PHE ARG VAL PRO TYR ASP PRO GLY LEU LYS SEQRES 51 A 960 ALA GLY ALA LEU ALA ILE GLU LYS CYS LYS VAL MET ALA SEQRES 52 A 960 SER LYS LYS LYS PRO LEU TRP LEU GLU PHE LYS CYS ALA SEQRES 53 A 960 ASP PRO THR ALA LEU SER ASN GLU THR ILE GLY ILE ILE SEQRES 54 A 960 PHE LYS HIS GLY ASP ASP LEU ARG GLN ASP MET LEU ILE SEQRES 55 A 960 LEU GLN ILE LEU ARG ILE MET GLU SER ILE TRP GLU THR SEQRES 56 A 960 GLU SER LEU ASP LEU CYS LEU LEU PRO TYR GLY CYS ILE SEQRES 57 A 960 SER THR GLY ASP LYS ILE GLY MET ILE GLU ILE VAL LYS SEQRES 58 A 960 ASP ALA THR THR ILE ALA LYS ILE GLN GLN SER THR VAL SEQRES 59 A 960 GLY ASN THR GLY ALA PHE LYS ASP GLU VAL LEU ASN HIS SEQRES 60 A 960 TRP LEU LYS GLU LYS SER PRO THR GLU GLU LYS PHE GLN SEQRES 61 A 960 ALA ALA VAL GLU ARG PHE VAL TYR SER CYS ALA GLY TYR SEQRES 62 A 960 CYS VAL ALA THR PHE VAL LEU GLY ILE GLY ASP ARG HIS SEQRES 63 A 960 ASN ASP ASN ILE MET ILE THR GLU THR GLY ASN LEU PHE SEQRES 64 A 960 HIS ILE ASP PHE GLY HIS ILE LEU GLY ASN TYR LYS SER SEQRES 65 A 960 PHE LEU GLY ILE ASN LYS GLU ARG VAL PRO PHE VAL LEU SEQRES 66 A 960 THR PRO ASP PHE LEU PHE VAL MET GLY THR SER GLY LYS SEQRES 67 A 960 LYS THR SER PRO HIS PHE GLN LYS PHE GLN ASP ILE CYS SEQRES 68 A 960 VAL LYS ALA TYR LEU ALA LEU ARG HIS HIS THR ASN LEU SEQRES 69 A 960 LEU ILE ILE LEU PHE SER MET MET LEU MET THR GLY MET SEQRES 70 A 960 PRO GLN LEU THR SER LYS GLU ASP ILE GLU TYR ILE ARG SEQRES 71 A 960 ASP ALA LEU THR VAL GLY LYS ASN GLU GLU ASP ALA LYS SEQRES 72 A 960 LYS TYR PHE LEU ASP GLN ILE GLU VAL CYS ARG ASP LYS SEQRES 73 A 960 GLY TRP THR VAL GLN PHE ASN TRP PHE LEU HIS LEU VAL SEQRES 74 A 960 LEU GLY ILE LYS GLN GLY GLU LYS HIS SER ALA HET GD9 A 1 35 HETNAM GD9 2-(1H-INDAZOL-4-YL)-6-{[4-(METHYLSULFONYL)PIPERAZIN-1- HETNAM 2 GD9 YL]METHYL}-4-MORPHOLIN-4-YL-THIENO[3,2-D]PYRIMIDINE FORMUL 2 GD9 C23 H27 N7 O3 S2 HELIX 1 1 SER A 144 GLY A 159 1 16 HELIX 2 2 ASP A 171 LEU A 180 1 10 HELIX 3 3 LEU A 180 SER A 190 1 11 HELIX 4 4 ASP A 192 HIS A 199 1 8 HELIX 5 5 PRO A 208 LYS A 213 1 6 HELIX 6 6 THR A 240 THR A 250 1 11 HELIX 7 7 PHE A 290 GLY A 300 1 11 HELIX 8 8 ASP A 312 GLU A 317 5 6 HELIX 9 9 ASN A 498 THR A 503 5 6 HELIX 10 10 PRO A 548 THR A 561 1 14 HELIX 11 11 THR A 568 PHE A 578 1 11 HELIX 12 12 PHE A 578 LEU A 583 1 6 HELIX 13 13 LYS A 584 LYS A 587 5 4 HELIX 14 14 ALA A 588 SER A 595 1 8 HELIX 15 15 GLN A 600 ARG A 613 1 14 HELIX 16 16 ARG A 614 SER A 620 1 7 HELIX 17 17 ASP A 623 LEU A 631 1 9 HELIX 18 18 ASP A 637 GLU A 649 1 13 HELIX 19 19 GLU A 652 ALA A 666 1 15 HELIX 20 20 VAL A 667 GLU A 670 5 4 HELIX 21 21 SER A 675 ASN A 688 1 14 HELIX 22 22 ASN A 688 SER A 706 1 19 HELIX 23 23 TYR A 709 ARG A 722 1 14 HELIX 24 24 GLY A 725 SER A 751 1 27 HELIX 25 25 SER A 760 ASN A 776 1 17 HELIX 26 26 ILE A 798 CYS A 801 5 4 HELIX 27 27 ASP A 837 THR A 857 1 21 HELIX 28 28 ILE A 888 GLN A 893 1 6 HELIX 29 29 GLU A 905 LYS A 914 1 10 HELIX 30 30 THR A 917 GLY A 943 1 27 HELIX 31 31 HIS A 948 ASP A 950 5 3 HELIX 32 32 THR A 988 MET A 995 1 8 HELIX 33 33 SER A 1003 HIS A 1022 1 20 HELIX 34 34 HIS A 1023 MET A 1039 1 17 HELIX 35 35 ILE A 1048 LEU A 1055 1 8 HELIX 36 36 ASN A 1060 GLY A 1079 1 20 HELIX 37 37 TRP A 1080 TRP A 1086 1 7 SHEET 1 A 5 THR A 232 VAL A 235 0 SHEET 2 A 5 ILE A 220 HIS A 225 -1 N ILE A 220 O VAL A 235 SHEET 3 A 5 ILE A 303 ASP A 308 1 O VAL A 305 N VAL A 223 SHEET 4 A 5 VAL A 271 VAL A 274 -1 N ARG A 273 O VAL A 306 SHEET 5 A 5 TYR A 280 LEU A 281 -1 O LEU A 281 N LEU A 272 SHEET 1 B 4 GLU A 407 LYS A 419 0 SHEET 2 B 4 LYS A 360 ASP A 369 -1 N PHE A 361 O ILE A 418 SHEET 3 B 4 SER A 515 LEU A 520 -1 O SER A 515 N ASP A 369 SHEET 4 B 4 GLY A 478 HIS A 483 -1 N GLY A 478 O LEU A 520 SHEET 1 C 3 GLN A 392 ARG A 398 0 SHEET 2 C 3 THR A 380 HIS A 389 -1 N HIS A 389 O GLN A 392 SHEET 3 C 3 LYS A 402 PRO A 403 -1 O LYS A 402 N VAL A 381 SHEET 1 D 5 GLN A 392 ARG A 398 0 SHEET 2 D 5 THR A 380 HIS A 389 -1 N HIS A 389 O GLN A 392 SHEET 3 D 5 LEU A 428 TYR A 434 -1 O GLN A 432 N GLU A 384 SHEET 4 D 5 TYR A 462 LEU A 467 -1 O LEU A 466 N LEU A 429 SHEET 5 D 5 TRP A 485 GLN A 486 -1 O TRP A 485 N TYR A 463 SHEET 1 E 4 PHE A 783 ARG A 784 0 SHEET 2 E 4 LYS A 792 LEU A 796 -1 O ALA A 793 N PHE A 783 SHEET 3 E 4 LEU A 811 CYS A 817 -1 O LYS A 816 N GLY A 794 SHEET 4 E 4 LYS A 802 VAL A 803 -1 N LYS A 802 O TRP A 812 SHEET 1 F 6 PHE A 783 ARG A 784 0 SHEET 2 F 6 LYS A 792 LEU A 796 -1 O ALA A 793 N PHE A 783 SHEET 3 F 6 LEU A 811 CYS A 817 -1 O LYS A 816 N GLY A 794 SHEET 4 F 6 ILE A 828 HIS A 834 -1 O ILE A 830 N LEU A 813 SHEET 5 F 6 ILE A 876 GLU A 880 -1 O ILE A 879 N ILE A 831 SHEET 6 F 6 CYS A 869 GLY A 873 -1 N ILE A 870 O MET A 878 SHEET 1 G 3 ALA A 885 THR A 887 0 SHEET 2 G 3 ILE A 952 THR A 955 -1 O ILE A 954 N THR A 886 SHEET 3 G 3 LEU A 960 HIS A 962 -1 O PHE A 961 N MET A 953 SITE 1 AC1 15 LYS A 802 MET A 804 ALA A 805 ILE A 831 SITE 2 AC1 15 LYS A 833 ASP A 836 ASP A 841 TYR A 867 SITE 3 AC1 15 ILE A 879 GLU A 880 ILE A 881 THR A 887 SITE 4 AC1 15 MET A 953 ILE A 963 ASP A 964 CRYST1 144.284 67.762 106.972 90.00 95.31 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 0.006931 0.000000 0.000644 0.00000 SCALE2 0.000000 0.014758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009389 0.00000