HEADER TRANSFERASE/TRANSFERASE INHIBITOR 26-JUN-15 5C9C TITLE CRYSTAL STRUCTURE OF BRAF(V600E) IN COMPLEX WITH LY3009120 COMPND COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE B-RAF; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 432-726; COMPND 5 SYNONYM: PROTO-ONCOGENE B-RAF,P94,V-RAF MURINE SARCOMA VIRAL ONCOGENE COMPND 6 HOMOLOG B1; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BRAF, BRAF1, RAFB1; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.EDWARDS,J.ABENDROTH,L.CHUN REVDAT 3 27-SEP-23 5C9C 1 JRNL REMARK REVDAT 2 14-OCT-15 5C9C 1 JRNL REVDAT 1 15-JUL-15 5C9C 0 JRNL AUTH S.B.PENG,J.R.HENRY,M.D.KAUFMAN,W.P.LU,B.D.SMITH,S.VOGETI, JRNL AUTH 2 T.J.RUTKOSKI,S.WISE,L.CHUN,Y.ZHANG,R.D.VAN HORN,T.YIN, JRNL AUTH 3 X.ZHANG,V.YADAV,S.H.CHEN,X.GONG,X.MA,Y.WEBSTER,S.BUCHANAN, JRNL AUTH 4 I.MOCHALKIN,L.HUBER,L.KAYS,G.P.DONOHO,J.WALGREN,D.MCCANN, JRNL AUTH 5 P.PATEL,I.CONTI,G.D.PLOWMAN,J.J.STARLING,D.L.FLYNN JRNL TITL INHIBITION OF RAF ISOFORMS AND ACTIVE DIMERS BY LY3009120 JRNL TITL 2 LEADS TO ANTI-TUMOR ACTIVITIES IN RAS OR BRAF MUTANT JRNL TITL 3 CANCERS. JRNL REF CANCER CELL V. 28 384 2015 JRNL REFN ISSN 1535-6108 JRNL PMID 26343583 JRNL DOI 10.1016/J.CCELL.2015.08.002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.HENRY,M.D.KAUFMAN,S.B.PENG,Y.M.AHN,T.M.CALDWELL, REMARK 1 AUTH 2 L.VOGETI,H.TELIKEPALLI,W.P.LU,M.M.HOOD,T.J.RUTKOSKI, REMARK 1 AUTH 3 B.D.SMITH,S.VOGETI,D.MILLER,S.C.WISE,L.CHUN,X.ZHANG,Y.ZHANG, REMARK 1 AUTH 4 L.KAYS,P.A.HIPSKIND,A.D.WROBLESKI,K.L.LOBB,J.M.CLAY, REMARK 1 AUTH 5 J.D.COHEN,J.L.WALGREN,D.MCCANN,P.PATEL,D.K.CLAWSON,S.GUO, REMARK 1 AUTH 6 D.MANGLICMOT,C.GROSHONG,C.LOGAN,J.J.STARLING,D.L.FLYNN REMARK 1 TITL DISCOVERY OF REMARK 1 TITL 2 1-(3,3-DIMETHYLBUTYL) REMARK 1 TITL 3 -3-(2-FLUORO-4-METHYL-5-(7-METHYL-2-(METHYLAMINO)PYRIDO[2, REMARK 1 TITL 4 3-D]PYRIMIDIN-6-YL)PHENYL)UREA (LY3009120) AS A PAN-RAF REMARK 1 TITL 5 INHIBITOR WITH MINIMAL PARADOXICAL ACTIVATION AND ACTIVITY REMARK 1 TITL 6 AGAINST BRAF OR RAS MUTANT TUMOR CELLS. REMARK 1 REF J.MED.CHEM. V. 58 4165 2015 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 25965804 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.5B00067 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20740 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1433 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3944 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : 0.57000 REMARK 3 B33 (A**2) : -1.13000 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): 0.623 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.301 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.913 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4108 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5570 ; 1.605 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 6.107 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;36.286 ;24.024 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 703 ;17.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.890 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3051 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2513 ; 0.833 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4041 ; 1.588 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1595 ; 2.103 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1527 ; 3.617 ; 4.500 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 : 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 REMARK 4 REMARK 4 5C9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL 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) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20853 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1UWH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 3350, 50 MM AMMONIUM CITRATE, REMARK 280 50 MM SODIUM FLORIDE, 2 MG/ML PROTEIN, 5-FOLD MOLAR EXCESS REMARK 280 DP4978; CRYSTAL ID 215552F10, SITTING DROP VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 82.77500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.94000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.38750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.94000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.16250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.38750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.94000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 124.16250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.77500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 419 REMARK 465 ASP A 420 REMARK 465 ARG A 421 REMARK 465 GLY A 422 REMARK 465 SER A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 HIS A 426 REMARK 465 HIS A 427 REMARK 465 HIS A 428 REMARK 465 HIS A 429 REMARK 465 GLY A 430 REMARK 465 SER A 431 REMARK 465 GLU A 432 REMARK 465 ASP A 433 REMARK 465 ARG A 434 REMARK 465 ASN A 435 REMARK 465 ARG A 436 REMARK 465 MET A 437 REMARK 465 LYS A 438 REMARK 465 THR A 439 REMARK 465 LEU A 440 REMARK 465 GLY A 441 REMARK 465 ARG A 442 REMARK 465 ARG A 443 REMARK 465 ASP A 444 REMARK 465 SER A 445 REMARK 465 SER A 446 REMARK 465 ASP A 447 REMARK 465 VAL A 486 REMARK 465 THR A 487 REMARK 465 GLU A 599 REMARK 465 LYS A 600 REMARK 465 SER A 601 REMARK 465 ARG A 602 REMARK 465 TRP A 603 REMARK 465 SER A 604 REMARK 465 GLY A 605 REMARK 465 SER A 606 REMARK 465 HIS A 607 REMARK 465 GLN A 608 REMARK 465 PHE A 609 REMARK 465 GLU A 610 REMARK 465 GLN A 611 REMARK 465 LEU A 612 REMARK 465 SER A 613 REMARK 465 GLY A 614 REMARK 465 LEU A 720 REMARK 465 PRO A 721 REMARK 465 LYS A 722 REMARK 465 ILE A 723 REMARK 465 HIS A 724 REMARK 465 ARG A 725 REMARK 465 MET B 419 REMARK 465 ASP B 420 REMARK 465 ARG B 421 REMARK 465 GLY B 422 REMARK 465 SER B 423 REMARK 465 HIS B 424 REMARK 465 HIS B 425 REMARK 465 HIS B 426 REMARK 465 HIS B 427 REMARK 465 HIS B 428 REMARK 465 HIS B 429 REMARK 465 GLY B 430 REMARK 465 SER B 431 REMARK 465 GLU B 432 REMARK 465 ASP B 433 REMARK 465 ARG B 434 REMARK 465 ASN B 435 REMARK 465 ARG B 436 REMARK 465 MET B 437 REMARK 465 LYS B 438 REMARK 465 THR B 439 REMARK 465 LEU B 440 REMARK 465 GLY B 441 REMARK 465 ARG B 442 REMARK 465 ARG B 443 REMARK 465 ASP B 444 REMARK 465 SER B 445 REMARK 465 SER B 446 REMARK 465 ASP B 447 REMARK 465 ALA B 597 REMARK 465 THR B 598 REMARK 465 GLU B 599 REMARK 465 LYS B 600 REMARK 465 SER B 601 REMARK 465 ARG B 602 REMARK 465 TRP B 603 REMARK 465 SER B 604 REMARK 465 GLY B 605 REMARK 465 SER B 606 REMARK 465 HIS B 607 REMARK 465 GLN B 608 REMARK 465 PHE B 609 REMARK 465 GLU B 610 REMARK 465 GLN B 611 REMARK 465 LEU B 612 REMARK 465 SER B 613 REMARK 465 GLY B 614 REMARK 465 GLN B 627 REMARK 465 ASP B 628 REMARK 465 LYS B 629 REMARK 465 LEU B 720 REMARK 465 PRO B 721 REMARK 465 LYS B 722 REMARK 465 ILE B 723 REMARK 465 HIS B 724 REMARK 465 ARG B 725 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 ASP A 453 CG OD1 OD2 REMARK 470 GLN A 460 CG CD OE1 NE2 REMARK 470 GLN A 492 CG CD OE1 NE2 REMARK 470 LYS A 546 CG CD CE NZ REMARK 470 MET A 626 CG SD CE REMARK 470 ASP A 628 CG OD1 OD2 REMARK 470 LYS A 629 CG CD CE NZ REMARK 470 LYS A 686 CG CD CE NZ REMARK 470 ARG A 690 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 699 CG CD CE NZ REMARK 470 ARG A 718 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 453 CG OD1 OD2 REMARK 470 GLN B 460 CG CD OE1 NE2 REMARK 470 ARG B 461 CG CD NE CZ NH1 NH2 REMARK 470 SER B 466 OG REMARK 470 PHE B 467 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 484 CG CD1 CD2 REMARK 470 ASN B 485 CG OD1 ND2 REMARK 470 LYS B 521 CG CD CE NZ REMARK 470 LYS B 546 CG CD CE NZ REMARK 470 ASP B 586 CG OD1 OD2 REMARK 470 ARG B 625 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 686 CG CD CE NZ REMARK 470 ARG B 690 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 718 CG CD NE CZ NH1 NH2 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 GLU A 544 58.11 38.08 REMARK 500 ARG A 574 -8.16 80.81 REMARK 500 ASP A 575 49.73 -155.40 REMARK 500 ASP A 676 94.17 -69.93 REMARK 500 TRP B 475 98.98 -162.48 REMARK 500 ASN B 485 24.50 -78.51 REMARK 500 ARG B 574 -12.16 73.35 REMARK 500 ASP B 575 46.53 -150.27 REMARK 500 LEU B 587 -64.60 -141.39 REMARK 500 TYR B 655 30.53 70.22 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 4Z5 A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4Z5 B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 802 DBREF 5C9C A 431 725 UNP P15056 BRAF_HUMAN 432 726 DBREF 5C9C B 431 725 UNP P15056 BRAF_HUMAN 432 726 SEQADV 5C9C MET A 419 UNP P15056 INITIATING METHIONINE SEQADV 5C9C ASP A 420 UNP P15056 EXPRESSION TAG SEQADV 5C9C ARG A 421 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLY A 422 UNP P15056 EXPRESSION TAG SEQADV 5C9C SER A 423 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 424 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 425 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 426 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 427 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 428 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS A 429 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLY A 430 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLU A 599 UNP P15056 VAL 600 ENGINEERED MUTATION SEQADV 5C9C MET B 419 UNP P15056 INITIATING METHIONINE SEQADV 5C9C ASP B 420 UNP P15056 EXPRESSION TAG SEQADV 5C9C ARG B 421 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLY B 422 UNP P15056 EXPRESSION TAG SEQADV 5C9C SER B 423 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 424 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 425 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 426 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 427 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 428 UNP P15056 EXPRESSION TAG SEQADV 5C9C HIS B 429 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLY B 430 UNP P15056 EXPRESSION TAG SEQADV 5C9C GLU B 599 UNP P15056 VAL 600 ENGINEERED MUTATION SEQRES 1 A 307 MET ASP ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER SEQRES 2 A 307 GLU ASP ARG ASN ARG MET LYS THR LEU GLY ARG ARG ASP SEQRES 3 A 307 SER SER ASP ASP TRP GLU ILE PRO ASP GLY GLN ILE THR SEQRES 4 A 307 VAL GLY GLN ARG ILE GLY SER GLY SER PHE GLY THR VAL SEQRES 5 A 307 TYR LYS GLY LYS TRP HIS GLY ASP VAL ALA VAL LYS MET SEQRES 6 A 307 LEU ASN VAL THR ALA PRO THR PRO GLN GLN LEU GLN ALA SEQRES 7 A 307 PHE LYS ASN GLU VAL GLY VAL LEU ARG LYS THR ARG HIS SEQRES 8 A 307 VAL ASN ILE LEU LEU PHE MET GLY TYR SER THR LYS PRO SEQRES 9 A 307 GLN LEU ALA ILE VAL THR GLN TRP CYS GLU GLY SER SER SEQRES 10 A 307 LEU TYR HIS HIS LEU HIS ILE ILE GLU THR LYS PHE GLU SEQRES 11 A 307 MET ILE LYS LEU ILE ASP ILE ALA ARG GLN THR ALA GLN SEQRES 12 A 307 GLY MET ASP TYR LEU HIS ALA LYS SER ILE ILE HIS ARG SEQRES 13 A 307 ASP LEU LYS SER ASN ASN ILE PHE LEU HIS GLU ASP LEU SEQRES 14 A 307 THR VAL LYS ILE GLY ASP PHE GLY LEU ALA THR GLU LYS SEQRES 15 A 307 SER ARG TRP SER GLY SER HIS GLN PHE GLU GLN LEU SER SEQRES 16 A 307 GLY SER ILE LEU TRP MET ALA PRO GLU VAL ILE ARG MET SEQRES 17 A 307 GLN ASP LYS ASN PRO TYR SER PHE GLN SER ASP VAL TYR SEQRES 18 A 307 ALA PHE GLY ILE VAL LEU TYR GLU LEU MET THR GLY GLN SEQRES 19 A 307 LEU PRO TYR SER ASN ILE ASN ASN ARG ASP GLN ILE ILE SEQRES 20 A 307 PHE MET VAL GLY ARG GLY TYR LEU SER PRO ASP LEU SER SEQRES 21 A 307 LYS VAL ARG SER ASN CYS PRO LYS ALA MET LYS ARG LEU SEQRES 22 A 307 MET ALA GLU CYS LEU LYS LYS LYS ARG ASP GLU ARG PRO SEQRES 23 A 307 LEU PHE PRO GLN ILE LEU ALA SER ILE GLU LEU LEU ALA SEQRES 24 A 307 ARG SER LEU PRO LYS ILE HIS ARG SEQRES 1 B 307 MET ASP ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER SEQRES 2 B 307 GLU ASP ARG ASN ARG MET LYS THR LEU GLY ARG ARG ASP SEQRES 3 B 307 SER SER ASP ASP TRP GLU ILE PRO ASP GLY GLN ILE THR SEQRES 4 B 307 VAL GLY GLN ARG ILE GLY SER GLY SER PHE GLY THR VAL SEQRES 5 B 307 TYR LYS GLY LYS TRP HIS GLY ASP VAL ALA VAL LYS MET SEQRES 6 B 307 LEU ASN VAL THR ALA PRO THR PRO GLN GLN LEU GLN ALA SEQRES 7 B 307 PHE LYS ASN GLU VAL GLY VAL LEU ARG LYS THR ARG HIS SEQRES 8 B 307 VAL ASN ILE LEU LEU PHE MET GLY TYR SER THR LYS PRO SEQRES 9 B 307 GLN LEU ALA ILE VAL THR GLN TRP CYS GLU GLY SER SER SEQRES 10 B 307 LEU TYR HIS HIS LEU HIS ILE ILE GLU THR LYS PHE GLU SEQRES 11 B 307 MET ILE LYS LEU ILE ASP ILE ALA ARG GLN THR ALA GLN SEQRES 12 B 307 GLY MET ASP TYR LEU HIS ALA LYS SER ILE ILE HIS ARG SEQRES 13 B 307 ASP LEU LYS SER ASN ASN ILE PHE LEU HIS GLU ASP LEU SEQRES 14 B 307 THR VAL LYS ILE GLY ASP PHE GLY LEU ALA THR GLU LYS SEQRES 15 B 307 SER ARG TRP SER GLY SER HIS GLN PHE GLU GLN LEU SER SEQRES 16 B 307 GLY SER ILE LEU TRP MET ALA PRO GLU VAL ILE ARG MET SEQRES 17 B 307 GLN ASP LYS ASN PRO TYR SER PHE GLN SER ASP VAL TYR SEQRES 18 B 307 ALA PHE GLY ILE VAL LEU TYR GLU LEU MET THR GLY GLN SEQRES 19 B 307 LEU PRO TYR SER ASN ILE ASN ASN ARG ASP GLN ILE ILE SEQRES 20 B 307 PHE MET VAL GLY ARG GLY TYR LEU SER PRO ASP LEU SER SEQRES 21 B 307 LYS VAL ARG SER ASN CYS PRO LYS ALA MET LYS ARG LEU SEQRES 22 B 307 MET ALA GLU CYS LEU LYS LYS LYS ARG ASP GLU ARG PRO SEQRES 23 B 307 LEU PHE PRO GLN ILE LEU ALA SER ILE GLU LEU LEU ALA SEQRES 24 B 307 ARG SER LEU PRO LYS ILE HIS ARG HET 4Z5 A 900 31 HET 4Z5 B 801 31 HET CL B 802 1 HETNAM 4Z5 1-(3,3-DIMETHYLBUTYL)-3-{2-FLUORO-4-METHYL-5-[7-METHYL- HETNAM 2 4Z5 2-(METHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-6-YL]PHENYL}UREA HETNAM CL CHLORIDE ION HETSYN 4Z5 LY3009120 FORMUL 3 4Z5 2(C23 H29 F N6 O) FORMUL 5 CL CL 1- FORMUL 6 HOH *135(H2 O) HELIX 1 AA1 THR A 490 ARG A 505 1 16 HELIX 2 AA2 LEU A 536 ILE A 542 1 7 HELIX 3 AA3 GLU A 548 LYS A 569 1 22 HELIX 4 AA4 LYS A 577 ASN A 579 5 3 HELIX 5 AA5 SER A 615 MET A 619 5 5 HELIX 6 AA6 ALA A 620 MET A 626 1 7 HELIX 7 AA7 SER A 633 GLY A 651 1 19 HELIX 8 AA8 ASN A 660 ARG A 670 1 11 HELIX 9 AA9 ASP A 676 VAL A 680 5 5 HELIX 10 AB1 PRO A 685 LEU A 696 1 12 HELIX 11 AB2 LYS A 699 ARG A 703 5 5 HELIX 12 AB3 LEU A 705 ARG A 718 1 14 HELIX 13 AB4 THR B 490 ARG B 505 1 16 HELIX 14 AB5 LEU B 536 ILE B 542 1 7 HELIX 15 AB6 GLU B 548 LYS B 569 1 22 HELIX 16 AB7 LYS B 577 ASN B 579 5 3 HELIX 17 AB8 SER B 615 MET B 619 5 5 HELIX 18 AB9 ALA B 620 ARG B 625 1 6 HELIX 19 AC1 SER B 633 GLY B 651 1 19 HELIX 20 AC2 ASN B 660 ARG B 670 1 11 HELIX 21 AC3 ASP B 676 VAL B 680 5 5 HELIX 22 AC4 PRO B 685 LEU B 696 1 12 HELIX 23 AC5 LYS B 699 ARG B 703 5 5 HELIX 24 AC6 LEU B 705 ARG B 718 1 14 SHEET 1 AA1 5 THR A 457 GLY A 465 0 SHEET 2 AA1 5 GLY A 468 LYS A 474 -1 O VAL A 470 N ILE A 462 SHEET 3 AA1 5 ASP A 478 MET A 483 -1 O VAL A 481 N TYR A 471 SHEET 4 AA1 5 ALA A 525 GLN A 529 -1 O ILE A 526 N LYS A 482 SHEET 5 AA1 5 PHE A 515 SER A 519 -1 N MET A 516 O VAL A 527 SHEET 1 AA2 3 GLY A 533 SER A 535 0 SHEET 2 AA2 3 ILE A 581 HIS A 584 -1 O LEU A 583 N SER A 534 SHEET 3 AA2 3 THR A 588 ILE A 591 -1 O LYS A 590 N PHE A 582 SHEET 1 AA3 5 THR B 457 GLY B 465 0 SHEET 2 AA3 5 GLY B 468 LYS B 474 -1 O VAL B 470 N ILE B 462 SHEET 3 AA3 5 ASP B 478 MET B 483 -1 O VAL B 479 N GLY B 473 SHEET 4 AA3 5 ALA B 525 GLN B 529 -1 O THR B 528 N ALA B 480 SHEET 5 AA3 5 PHE B 515 SER B 519 -1 N GLY B 517 O VAL B 527 SHEET 1 AA4 3 GLY B 533 SER B 535 0 SHEET 2 AA4 3 ILE B 581 HIS B 584 -1 O LEU B 583 N SER B 534 SHEET 3 AA4 3 THR B 588 ILE B 591 -1 O LYS B 590 N PHE B 582 CISPEP 1 LYS A 521 PRO A 522 0 -2.83 CISPEP 2 LYS A 629 ASN A 630 0 0.99 CISPEP 3 LYS B 521 PRO B 522 0 -3.76 SITE 1 AC1 12 ALA A 480 LYS A 482 GLU A 500 LEU A 504 SITE 2 AC1 12 LEU A 513 ILE A 526 THR A 528 GLN A 529 SITE 3 AC1 12 CYS A 531 GLY A 592 ASP A 593 PHE A 594 SITE 1 AC2 14 VAL B 470 ALA B 480 LYS B 482 GLU B 500 SITE 2 AC2 14 LEU B 504 LEU B 513 ILE B 526 THR B 528 SITE 3 AC2 14 GLN B 529 TRP B 530 CYS B 531 HIS B 573 SITE 4 AC2 14 GLY B 592 ASP B 593 SITE 1 AC3 3 TRP A 449 ARG A 505 ARG B 505 CRYST1 93.880 93.880 165.550 90.00 90.00 90.00 P 41 21 2 16 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 0.010652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006040 0.00000