HEADER TRANSFERASE 02-JAN-07 2OF4 TITLE CRYSTAL STRUCTURE OF FURANOPYRIMIDINE 1 BOUND TO LCK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LCK KINASE DOMAIN, RESIDUES 230-500; COMPND 5 SYNONYM: P56-LCK, LYMPHOCYTE CELL-SPECIFIC PROTEIN-TYROSINE KINASE, COMPND 6 LSK, T CELL- SPECIFIC PROTEIN-TYROSINE KINASE; COMPND 7 EC: 2.7.10.2; COMPND 8 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: LCK; SOURCE 6 EXPRESSION_SYSTEM: INSECT CELL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS LCK, KINASE DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.W.MARTIN REVDAT 4 30-AUG-23 2OF4 1 REMARK REVDAT 3 24-FEB-09 2OF4 1 VERSN REVDAT 2 24-APR-07 2OF4 1 JRNL REVDAT 1 27-FEB-07 2OF4 0 JRNL AUTH M.W.MARTIN,J.NEWCOMB,J.J.NUNES,J.E.BEMIS,D.C.MCGOWAN, JRNL AUTH 2 R.D.WHITE,J.L.BUCHANAN,E.F.DIMAURO,C.BOUCHER,T.FAUST, JRNL AUTH 3 F.HSIEH,X.HUANG,J.H.LEE,S.SCHNEIDER,S.M.TURCI,X.ZHU JRNL TITL DISCOVERY OF NOVEL 2,3-DIARYLFURO[2,3-B]PYRIDIN-4-AMINES AS JRNL TITL 2 POTENT AND SELECTIVE INHIBITORS OF LCK: SYNTHESIS, SAR, AND JRNL TITL 3 PHARMACOKINETIC PROPERTIES. JRNL REF BIOORG.MED.CHEM.LETT. V. 17 2299 2007 JRNL REFN ISSN 0960-894X JRNL PMID 17276681 JRNL DOI 10.1016/J.BMCL.2007.01.048 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 7372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 402 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 44 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.475 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 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) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 1QPC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI2SO4, 25-35% PEG4000, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.80000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER AS OBSERVED. 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 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 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 GLN A 309 CG CD OE1 NE2 REMARK 470 ARG A 397 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 PRO A 447 CG CD REMARK 470 GLN A 451 CG CD OE1 NE2 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 VAL A 272 CB REMARK 480 PHE A 426 O 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 363 -5.33 70.92 REMARK 500 ASP A 382 89.20 53.91 REMARK 500 ALA A 396 -169.11 -71.96 REMARK 500 GLU A 398 -34.53 -39.08 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 615 979 A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OF2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH FURANOPYRIDINE 8 DBREF 2OF4 A 231 501 UNP P06239 LCK_HUMAN 230 500 SEQRES 1 A 271 LYS PRO TRP TRP GLU ASP GLU TRP GLU VAL PRO ARG GLU SEQRES 2 A 271 THR LEU LYS LEU VAL GLU ARG LEU GLY ALA GLY GLN PHE SEQRES 3 A 271 GLY GLU VAL TRP MET GLY TYR TYR ASN GLY HIS THR LYS SEQRES 4 A 271 VAL ALA VAL LYS SER LEU LYS GLN GLY SER MET SER PRO SEQRES 5 A 271 ASP ALA PHE LEU ALA GLU ALA ASN LEU MET LYS GLN LEU SEQRES 6 A 271 GLN HIS GLN ARG LEU VAL ARG LEU TYR ALA VAL VAL THR SEQRES 7 A 271 GLN GLU PRO ILE TYR ILE ILE THR GLU TYR MET GLU ASN SEQRES 8 A 271 GLY SER LEU VAL ASP PHE LEU LYS THR PRO SER GLY ILE SEQRES 9 A 271 LYS LEU THR ILE ASN LYS LEU LEU ASP MET ALA ALA GLN SEQRES 10 A 271 ILE ALA GLU GLY MET ALA PHE ILE GLU GLU ARG ASN TYR SEQRES 11 A 271 ILE HIS ARG ASP LEU ARG ALA ALA ASN ILE LEU VAL SER SEQRES 12 A 271 ASP THR LEU SER CYS LYS ILE ALA ASP PHE GLY LEU ALA SEQRES 13 A 271 ARG LEU ILE GLU ASP ASN GLU TYR THR ALA ARG GLU GLY SEQRES 14 A 271 ALA LYS PHE PRO ILE LYS TRP THR ALA PRO GLU ALA ILE SEQRES 15 A 271 ASN TYR GLY THR PHE THR ILE LYS SER ASP VAL TRP SER SEQRES 16 A 271 PHE GLY ILE LEU LEU THR GLU ILE VAL THR HIS GLY ARG SEQRES 17 A 271 ILE PRO TYR PRO GLY MET THR ASN PRO GLU VAL ILE GLN SEQRES 18 A 271 ASN LEU GLU ARG GLY TYR ARG MET VAL ARG PRO ASP ASN SEQRES 19 A 271 CYS PRO GLU GLU LEU TYR GLN LEU MET ARG LEU CYS TRP SEQRES 20 A 271 LYS GLU ARG PRO GLU ASP ARG PRO THR PHE ASP TYR LEU SEQRES 21 A 271 ARG SER VAL LEU GLU ASP PHE PHE THR ALA THR HET 979 A 101 30 HETNAM 979 5,6-DIPHENYL-N-(2-PIPERAZIN-1-YLETHYL)FURO[2,3- HETNAM 2 979 D]PYRIMIDIN-4-AMINE HETSYN 979 FURANOPYRIDIMIDINE 1 FORMUL 2 979 C24 H25 N5 O FORMUL 3 HOH *44(H2 O) HELIX 1 1 PRO A 241 GLU A 243 5 3 HELIX 2 2 SER A 281 GLN A 294 1 14 HELIX 3 3 SER A 323 LEU A 328 1 6 HELIX 4 4 THR A 330 LEU A 336 1 7 HELIX 5 5 THR A 337 ALA A 353 1 17 HELIX 6 6 PHE A 354 GLU A 356 1 3 HELIX 7 7 ARG A 366 ALA A 368 5 3 HELIX 8 8 PRO A 403 THR A 407 5 5 HELIX 9 9 ALA A 408 GLY A 415 1 8 HELIX 10 10 THR A 418 THR A 435 1 18 HELIX 11 11 THR A 445 ARG A 455 1 11 HELIX 12 12 PRO A 466 TRP A 477 1 12 HELIX 13 13 ARG A 480 ARG A 484 5 5 HELIX 14 14 THR A 486 THR A 501 1 16 SHEET 1 A 5 LEU A 245 GLY A 254 0 SHEET 2 A 5 GLY A 257 TYR A 264 -1 O MET A 261 N GLU A 249 SHEET 3 A 5 THR A 268 LEU A 275 -1 O THR A 268 N TYR A 264 SHEET 4 A 5 TYR A 313 GLU A 317 -1 O THR A 316 N ALA A 271 SHEET 5 A 5 LEU A 303 VAL A 307 -1 N TYR A 304 O ILE A 315 SHEET 1 B 2 TYR A 360 ILE A 361 0 SHEET 2 B 2 ARG A 387 LEU A 388 -1 O ARG A 387 N ILE A 361 SHEET 1 C 2 ILE A 370 VAL A 372 0 SHEET 2 C 2 CYS A 378 ILE A 380 -1 O LYS A 379 N LEU A 371 SHEET 1 D 2 TYR A 394 THR A 395 0 SHEET 2 D 2 THR A 416 PHE A 417 -1 O PHE A 417 N TYR A 394 CISPEP 1 GLU A 310 PRO A 311 0 -1.37 CRYST1 42.100 73.600 91.900 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 0.023753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010881 0.00000