HEADER TRANSFERASE/TRANSFERASE INHIBITOR 18-MAY-18 6DGT TITLE SELECTIVE PI3K BETA INHIBITOR BOUND TO PI3K DELTA 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 FRAGMENT: RESIDUES 106-1043; COMPND 6 SYNONYM: PTDINS-3-KINASE SUBUNIT DELTA,PHOSPHATIDYLINOSITOL 4,5- COMPND 7 BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT DELTA,P110DELTA; COMPND 8 EC: 2.7.1.153; COMPND 9 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PI3K DELTA, P110, INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.SOMOZA,A.VILLASENOR,M.MCGRATH REVDAT 3 13-MAR-24 6DGT 1 REMARK REVDAT 2 22-AUG-18 6DGT 1 JRNL REVDAT 1 01-AUG-18 6DGT 0 JRNL AUTH J.CHANDRASEKHAR,R.DICK,J.VAN VELDHUIZEN,D.KODITEK, JRNL AUTH 2 E.I.LEPIST,M.E.MCGRATH,L.PATEL,G.PHILLIPS,K.SEDILLO, JRNL AUTH 3 J.R.SOMOZA,J.THERRIEN,N.A.TILL,J.TREIBERG,A.G.VILLASENOR, JRNL AUTH 4 Y.ZHEREBINA,S.PERREAULT JRNL TITL ATROPISOMERISM BY DESIGN: DISCOVERY OF A SELECTIVE AND JRNL TITL 2 STABLE PHOSPHOINOSITIDE 3-KINASE (PI3K) BETA INHIBITOR. JRNL REF J. MED. CHEM. V. 61 6858 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30015489 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00797 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 31431 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.0604 - 6.2614 0.99 2223 151 0.2194 0.2695 REMARK 3 2 6.2614 - 4.9729 1.00 2140 146 0.2269 0.3438 REMARK 3 3 4.9729 - 4.3451 1.00 2134 144 0.1959 0.2818 REMARK 3 4 4.3451 - 3.9482 1.00 2102 143 0.1898 0.2928 REMARK 3 5 3.9482 - 3.6654 1.00 2126 145 0.2077 0.2640 REMARK 3 6 3.6654 - 3.4495 1.00 2107 143 0.2329 0.3145 REMARK 3 7 3.4495 - 3.2768 1.00 2075 141 0.2517 0.3776 REMARK 3 8 3.2768 - 3.1342 1.00 2086 142 0.2554 0.3690 REMARK 3 9 3.1342 - 3.0136 1.00 2090 141 0.2919 0.3850 REMARK 3 10 3.0136 - 2.9096 1.00 2083 142 0.2776 0.4095 REMARK 3 11 2.9096 - 2.8187 1.00 2104 143 0.2913 0.3752 REMARK 3 12 2.8187 - 2.7381 1.00 2080 141 0.3031 0.4048 REMARK 3 13 2.7381 - 2.6661 1.00 2077 141 0.3027 0.3789 REMARK 3 14 2.6661 - 2.6010 0.96 2005 136 0.3084 0.3764 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 6397 REMARK 3 ANGLE : 1.894 8642 REMARK 3 CHIRALITY : 0.084 958 REMARK 3 PLANARITY : 0.011 1090 REMARK 3 DIHEDRAL : 16.753 3832 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JAN-16 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 : SSRL REMARK 200 BEAMLINE : BL7-1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 152619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4670 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 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: NULL REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 300, 0.1M TRIS PH 8.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 110.62800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 110.62800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.75850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.75100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.75850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.75100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 110.62800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.75850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.75100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 110.62800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.75850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.75100 REMARK 290 SMTRY3 8 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 GLY A 106 REMARK 465 ASP A 107 REMARK 465 ARG A 108 REMARK 465 VAL A 109 REMARK 465 LYS A 110 REMARK 465 HIS A 126 REMARK 465 GLU A 127 REMARK 465 PHE A 128 REMARK 465 SER A 174 REMARK 465 ALA A 175 REMARK 465 ARG A 176 REMARK 465 GLY A 177 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 ASN A 187 REMARK 465 ARG A 188 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 LYS A 223 REMARK 465 LYS A 224 REMARK 465 ALA A 225 REMARK 465 THR A 226 REMARK 465 VAL A 227 REMARK 465 PHE A 228 REMARK 465 ARG A 229 REMARK 465 GLN A 230 REMARK 465 PRO A 231 REMARK 465 LEU A 232 REMARK 465 VAL A 233 REMARK 465 GLU A 234 REMARK 465 TYR A 251 REMARK 465 GLY A 252 REMARK 465 ASN A 253 REMARK 465 PRO A 292 REMARK 465 ALA A 293 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 SER A 315 REMARK 465 LEU A 316 REMARK 465 TRP A 317 REMARK 465 ASN A 334 REMARK 465 ALA A 335 REMARK 465 ASP A 336 REMARK 465 GLU A 337 REMARK 465 ARG A 338 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 ASP A 415 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 PRO A 480 REMARK 465 HIS A 481 REMARK 465 GLY A 496 REMARK 465 ARG A 497 REMARK 465 HIS A 498 REMARK 465 GLY A 499 REMARK 465 GLU A 500 REMARK 465 ARG A 501 REMARK 465 GLY A 502 REMARK 465 ARG A 503 REMARK 465 ILE A 504 REMARK 465 THR A 505 REMARK 465 GLU A 506 REMARK 465 GLU A 507 REMARK 465 GLU A 508 REMARK 465 LEU A 509 REMARK 465 GLN A 510 REMARK 465 LEU A 511 REMARK 465 ARG A 512 REMARK 465 GLU A 513 REMARK 465 ILE A 514 REMARK 465 LEU A 515 REMARK 465 GLU A 516 REMARK 465 ARG A 517 REMARK 465 ARG A 518 REMARK 465 GLY A 519 REMARK 465 SER A 520 REMARK 465 GLY A 521 REMARK 465 GLU A 522 REMARK 465 LEU A 523 REMARK 465 LYS A 841 REMARK 465 SER A 842 REMARK 465 ASN A 843 REMARK 465 MET A 844 REMARK 465 ALA A 845 REMARK 465 ALA A 846 REMARK 465 THR A 847 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 ARG A 927 REMARK 465 GLU A 928 REMARK 465 ARG A 929 REMARK 465 SER A 1026 REMARK 465 TRP A 1027 REMARK 465 LYS A 1028 REMARK 465 THR A 1029 REMARK 465 LYS A 1030 REMARK 465 VAL A 1031 REMARK 465 ASN A 1032 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 LYS A 111 CG CD CE NZ REMARK 470 LEU A 112 CG CD1 CD2 REMARK 470 SER A 115 OG REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 HIS A 153 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 206 CG CD OE1 NE2 REMARK 470 LYS A 210 CG CD CE NZ REMARK 470 CYS A 257 SG REMARK 470 GLN A 260 CG CD OE1 NE2 REMARK 470 SER A 264 OG REMARK 470 LEU A 266 CG CD1 CD2 REMARK 470 LEU A 452 CG CD1 CD2 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 OD2 ASP A 138 OH TYR A 428 1.95 REMARK 500 OE1 GLU A 326 NZ LYS A 372 2.00 REMARK 500 NH2 ARG A 437 O HOH A 1201 2.08 REMARK 500 O ILE A 872 OG1 THR A 876 2.09 REMARK 500 OE1 GLU A 722 O HOH A 1202 2.10 REMARK 500 NE2 GLN A 786 O HIS A 914 2.15 REMARK 500 O GLY A 435 N LEU A 475 2.19 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 CYS A 265 CB CYS A 265 SG 0.114 REMARK 500 GLU A 477 CD GLU A 477 OE1 -0.067 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 MET A 387 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 LEU A 494 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 MET A 534 CA - CB - CG ANGL. DEV. = 21.1 DEGREES REMARK 500 MET A 564 CG - SD - CE ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 652 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 663 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU A 907 CA - CB - CG ANGL. DEV. = 15.3 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 ARG A 132 58.88 18.08 REMARK 500 GLU A 237 -4.60 -58.00 REMARK 500 GLN A 260 -55.32 -18.86 REMARK 500 LEU A 266 -76.94 -53.64 REMARK 500 HIS A 267 -15.72 -32.61 REMARK 500 ILE A 325 -158.11 -104.43 REMARK 500 ILE A 328 -80.02 -60.40 REMARK 500 ARG A 331 -3.67 -145.30 REMARK 500 ASN A 351 48.94 -98.33 REMARK 500 CYS A 355 -150.76 -174.90 REMARK 500 VAL A 365 -75.82 -36.73 REMARK 500 SER A 367 -171.85 142.23 REMARK 500 TRP A 371 -52.15 -138.09 REMARK 500 LYS A 372 59.43 36.81 REMARK 500 ILE A 418 -65.92 -128.84 REMARK 500 ASP A 430 16.04 81.72 REMARK 500 ALA A 487 162.05 -48.67 REMARK 500 LYS A 533 -126.35 42.77 REMARK 500 LEU A 546 -63.67 -26.67 REMARK 500 THR A 553 126.68 -37.06 REMARK 500 SER A 586 26.75 -79.53 REMARK 500 GLU A 722 -83.63 3.34 REMARK 500 ASP A 736 99.08 -177.44 REMARK 500 GLU A 742 -96.48 -97.28 REMARK 500 ASP A 753 54.82 -90.40 REMARK 500 LYS A 755 -95.54 109.46 REMARK 500 GLU A 804 27.11 -140.33 REMARK 500 ASP A 911 90.26 43.89 REMARK 500 PHE A 912 -67.79 -95.30 REMARK 500 HIS A 914 -108.16 -105.21 REMARK 500 PHE A 915 168.14 82.77 REMARK 500 LEU A 934 140.20 -179.00 REMARK 500 THR A 947 -67.01 -5.74 REMARK 500 HIS A 970 34.77 -86.54 REMARK 500 LEU A 989 56.93 -115.31 REMARK 500 CYS A 991 -158.78 -118.08 REMARK 500 ALA A1003 50.56 27.78 REMARK 500 ARG A1024 16.85 -62.01 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 LEU A 530 VAL A 531 146.81 REMARK 500 TRP A 532 LYS A 533 129.69 REMARK 500 SER A 754 LYS A 755 137.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET A 534 16.05 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 GFJ A 1101 DBREF 6DGT A 106 1044 UNP O35904 PK3CD_MOUSE 106 1043 SEQRES 1 A 938 GLY ASP ARG VAL LYS LYS LEU ILE ASN SER GLN ILE SER SEQRES 2 A 938 LEU LEU ILE GLY LYS GLY LEU HIS GLU PHE ASP SER LEU SEQRES 3 A 938 ARG ASP PRO GLU VAL ASN ASP PHE ARG THR LYS MET ARG SEQRES 4 A 938 GLN PHE CYS GLU GLU ALA ALA ALA HIS ARG GLN GLN LEU SEQRES 5 A 938 GLY TRP VAL GLU TRP LEU GLN TYR SER PHE PRO LEU GLN SEQRES 6 A 938 LEU GLU PRO SER ALA ARG GLY TRP ARG ALA GLY LEU LEU SEQRES 7 A 938 ARG VAL SER ASN ARG ALA LEU LEU VAL ASN VAL LYS PHE SEQRES 8 A 938 GLU GLY SER GLU GLU SER PHE THR PHE GLN VAL SER THR SEQRES 9 A 938 LYS ASP MET PRO LEU ALA LEU MET ALA CYS ALA LEU ARG SEQRES 10 A 938 LYS LYS ALA THR VAL PHE ARG GLN PRO LEU VAL GLU GLN SEQRES 11 A 938 PRO GLU GLU TYR ALA LEU GLN VAL ASN GLY ARG HIS GLU SEQRES 12 A 938 TYR LEU TYR GLY ASN TYR PRO LEU CYS HIS PHE GLN TYR SEQRES 13 A 938 ILE CYS SER CYS LEU HIS SER GLY LEU THR PRO HIS LEU SEQRES 14 A 938 THR MET VAL HIS SER SER SER ILE LEU ALA MET ARG ASP SEQRES 15 A 938 GLU GLN SER ASN PRO ALA PRO GLN VAL GLN LYS PRO ARG SEQRES 16 A 938 ALA LYS PRO PRO PRO ILE PRO ALA LYS LYS PRO SER SER SEQRES 17 A 938 VAL SER LEU TRP SER LEU GLU GLN PRO PHE SER ILE GLU SEQRES 18 A 938 LEU ILE GLU GLY ARG LYS VAL ASN ALA ASP GLU ARG MET SEQRES 19 A 938 LYS LEU VAL VAL GLN ALA GLY LEU PHE HIS GLY ASN GLU SEQRES 20 A 938 MET LEU CYS LYS THR VAL SER SER SER GLU VAL ASN VAL SEQRES 21 A 938 CYS SER GLU PRO VAL TRP LYS GLN ARG LEU GLU PHE ASP SEQRES 22 A 938 ILE SER VAL CYS ASP LEU PRO ARG MET ALA ARG LEU CYS SEQRES 23 A 938 PHE ALA LEU TYR ALA VAL VAL GLU LYS ALA LYS LYS ALA SEQRES 24 A 938 ARG SER THR LYS LYS LYS SER LYS LYS ALA ASP CYS PRO SEQRES 25 A 938 ILE ALA TRP ALA ASN LEU MET LEU PHE ASP TYR LYS ASP SEQRES 26 A 938 GLN LEU LYS THR GLY GLU ARG CYS LEU TYR MET TRP PRO SEQRES 27 A 938 SER VAL PRO ASP GLU LYS GLY GLU LEU LEU ASN PRO ALA SEQRES 28 A 938 GLY THR VAL ARG GLY ASN PRO ASN THR GLU SER ALA ALA SEQRES 29 A 938 ALA LEU VAL ILE TYR LEU PRO GLU VAL ALA PRO HIS PRO SEQRES 30 A 938 VAL TYR PHE PRO ALA LEU GLU LYS ILE LEU GLU LEU GLY SEQRES 31 A 938 ARG HIS GLY GLU ARG GLY ARG ILE THR GLU GLU GLU LEU SEQRES 32 A 938 GLN LEU ARG GLU ILE LEU GLU ARG ARG GLY SER GLY GLU SEQRES 33 A 938 LEU TYR GLU HIS GLU LYS ASP LEU VAL TRP LYS MET ARG SEQRES 34 A 938 HIS GLU VAL GLN GLU HIS PHE PRO GLU ALA LEU ALA ARG SEQRES 35 A 938 LEU LEU LEU VAL THR LYS TRP ASN LYS HIS GLU ASP VAL SEQRES 36 A 938 ALA GLN MET LEU TYR LEU LEU CYS SER TRP PRO GLU LEU SEQRES 37 A 938 PRO VAL LEU SER ALA LEU GLU LEU LEU ASP PHE SER PHE SEQRES 38 A 938 PRO ASP CYS TYR VAL GLY SER PHE ALA ILE LYS SER LEU SEQRES 39 A 938 ARG LYS LEU THR ASP ASP GLU LEU PHE GLN TYR LEU LEU SEQRES 40 A 938 GLN LEU VAL GLN VAL LEU LYS TYR GLU SER TYR LEU ASP SEQRES 41 A 938 CYS GLU LEU THR LYS PHE LEU LEU GLY ARG ALA LEU ALA SEQRES 42 A 938 ASN ARG LYS ILE GLY HIS PHE LEU PHE TRP HIS LEU ARG SEQRES 43 A 938 SER GLU MET HIS VAL PRO SER VAL ALA LEU ARG PHE GLY SEQRES 44 A 938 LEU ILE MET GLU ALA TYR CYS ARG GLY SER THR HIS HIS SEQRES 45 A 938 MET LYS VAL LEU MET LYS GLN GLY GLU ALA LEU SER LYS SEQRES 46 A 938 LEU LYS ALA LEU ASN ASP PHE VAL LYS VAL SER SER GLN SEQRES 47 A 938 LYS THR THR LYS PRO GLN THR LYS GLU MET MET HIS MET SEQRES 48 A 938 CYS MET ARG GLN GLU THR TYR MET GLU ALA LEU SER HIS SEQRES 49 A 938 LEU GLN SER PRO LEU ASP PRO SER THR LEU LEU GLU GLU SEQRES 50 A 938 VAL CYS VAL GLU GLN CYS THR PHE MET ASP SER LYS MET SEQRES 51 A 938 LYS PRO LEU TRP ILE MET TYR SER SER GLU GLU ALA GLY SEQRES 52 A 938 SER ALA GLY ASN VAL GLY ILE ILE PHE LYS ASN GLY ASP SEQRES 53 A 938 ASP LEU ARG GLN ASP MET LEU THR LEU GLN MET ILE GLN SEQRES 54 A 938 LEU MET ASP VAL LEU TRP LYS GLN GLU GLY LEU ASP LEU SEQRES 55 A 938 ARG MET THR PRO TYR GLY CYS LEU PRO THR GLY ASP ARG SEQRES 56 A 938 THR GLY LEU ILE GLU VAL VAL LEU HIS SER ASP THR ILE SEQRES 57 A 938 ALA ASN ILE GLN LEU ASN LYS SER ASN MET ALA ALA THR SEQRES 58 A 938 ALA ALA PHE ASN LYS ASP ALA LEU LEU ASN TRP LEU LYS SEQRES 59 A 938 SER LYS ASN PRO GLY GLU ALA LEU ASP ARG ALA ILE GLU SEQRES 60 A 938 GLU PHE THR LEU SER CYS ALA GLY TYR CYS VAL ALA THR SEQRES 61 A 938 TYR VAL LEU GLY ILE GLY ASP ARG HIS SER ASP ASN ILE SEQRES 62 A 938 MET ILE ARG GLU SER GLY GLN LEU PHE HIS ILE ASP PHE SEQRES 63 A 938 GLY HIS PHE LEU GLY ASN PHE LYS THR LYS PHE GLY ILE SEQRES 64 A 938 ASN ARG GLU ARG VAL PRO PHE ILE LEU THR TYR ASP PHE SEQRES 65 A 938 VAL HIS VAL ILE GLN GLN GLY LYS THR ASN ASN SER GLU SEQRES 66 A 938 LYS PHE GLU ARG PHE ARG GLY TYR CYS GLU ARG ALA TYR SEQRES 67 A 938 THR ILE LEU ARG ARG HIS GLY LEU LEU PHE LEU HIS LEU SEQRES 68 A 938 PHE ALA LEU MET ARG ALA ALA GLY LEU PRO GLU LEU SER SEQRES 69 A 938 CYS SER LYS ASP ILE GLN TYR LEU LYS ASP SER LEU ALA SEQRES 70 A 938 LEU GLY LYS THR GLU GLU GLU ALA LEU LYS HIS PHE ARG SEQRES 71 A 938 VAL LYS PHE ASN GLU ALA LEU ARG GLU SER TRP LYS THR SEQRES 72 A 938 LYS VAL ASN TRP LEU ALA HIS ASN VAL SER LYS ASP ASN SEQRES 73 A 938 ARG GLN HET GFJ A1101 35 HETNAM GFJ 4-[1-(5,8-DIFLUOROQUINOLIN-4-YL)-2-METHYL-4-(4H-1,2,4- HETNAM 2 GFJ TRIAZOL-3-YL)-1H-BENZIMIDAZOL-6-YL]-3-FLUOROPYRIDIN-2- HETNAM 3 GFJ AMINE FORMUL 2 GFJ C24 H15 F3 N8 FORMUL 3 HOH *43(H2 O) HELIX 1 AA1 LYS A 111 GLY A 122 1 12 HELIX 2 AA2 ASP A 133 GLN A 156 1 24 HELIX 3 AA3 GLY A 158 PHE A 167 1 10 HELIX 4 AA4 MET A 212 ARG A 222 1 11 HELIX 5 AA5 GLN A 235 GLU A 237 5 3 HELIX 6 AA6 PRO A 255 HIS A 258 5 4 HELIX 7 AA7 PHE A 259 HIS A 267 1 9 HELIX 8 AA8 SER A 279 GLN A 289 1 11 HELIX 9 AA9 CYS A 382 LEU A 384 5 3 HELIX 10 AB1 ALA A 487 LEU A 494 1 8 HELIX 11 AB2 GLU A 525 LYS A 533 1 9 HELIX 12 AB3 MET A 534 PHE A 542 1 9 HELIX 13 AB4 ALA A 545 LEU A 551 1 7 HELIX 14 AB5 LYS A 557 CYS A 569 1 13 HELIX 15 AB6 PRO A 575 LEU A 583 1 9 HELIX 16 AB7 ASP A 589 SER A 599 1 11 HELIX 17 AB8 THR A 604 LEU A 619 1 16 HELIX 18 AB9 LYS A 620 GLU A 622 5 3 HELIX 19 AC1 CYS A 627 LEU A 638 1 12 HELIX 20 AC2 ASN A 640 SER A 653 1 14 HELIX 21 AC3 VAL A 657 SER A 675 1 19 HELIX 22 AC4 SER A 675 GLN A 704 1 30 HELIX 23 AC5 THR A 707 GLN A 721 1 15 HELIX 24 AC6 GLN A 721 LEU A 728 1 8 HELIX 25 AC7 VAL A 746 CYS A 749 5 4 HELIX 26 AC8 ALA A 768 ASN A 773 5 6 HELIX 27 AC9 LEU A 784 GLN A 803 1 20 HELIX 28 AD1 ILE A 834 LEU A 839 1 6 HELIX 29 AD2 PHE A 850 ASN A 863 1 14 HELIX 30 AD3 PRO A 864 GLU A 866 5 3 HELIX 31 AD4 ALA A 867 LEU A 889 1 23 HELIX 32 AD5 THR A 935 GLN A 943 1 9 HELIX 33 AD6 ASN A 949 HIS A 970 1 22 HELIX 34 AD7 HIS A 970 ARG A 982 1 13 HELIX 35 AD8 ALA A 983 GLY A 985 5 3 HELIX 36 AD9 LEU A 986 SER A 990 5 5 HELIX 37 AE1 CYS A 991 LEU A 1002 1 12 HELIX 38 AE2 THR A 1007 ALA A 1022 1 16 SHEET 1 AA1 5 SER A 202 VAL A 207 0 SHEET 2 AA1 5 LEU A 190 PHE A 196 -1 N VAL A 194 O PHE A 203 SHEET 3 AA1 5 HIS A 273 HIS A 278 1 O MET A 276 N LYS A 195 SHEET 4 AA1 5 TYR A 239 VAL A 243 -1 N GLN A 242 O THR A 275 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 GLY A 330 -1 N ILE A 328 O LYS A 372 SHEET 3 AA2 4 ALA A 470 LEU A 475 -1 O TYR A 474 N GLU A 326 SHEET 4 AA2 4 GLY A 435 TYR A 440 -1 N GLY A 435 O LEU A 475 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 VAL A 397 N LYS A 340 SHEET 4 AA4 5 PRO A 417 MET A 424 -1 O ALA A 421 N PHE A 392 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 THR A 818 O THR A 822 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 CISPEP 1 SER A 367 GLU A 368 0 -2.91 SITE 1 AC1 13 PHE A 751 MET A 752 PRO A 758 ILE A 777 SITE 2 AC1 13 LYS A 779 ASP A 787 ILE A 825 GLU A 826 SITE 3 AC1 13 VAL A 827 VAL A 828 SER A 831 MET A 900 SITE 4 AC1 13 ASP A 911 CRYST1 63.517 143.502 221.256 90.00 90.00 90.00 C 2 2 21 8 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 0.015744 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004520 0.00000