HEADER TRANSFERASE 20-OCT-05 2BDJ TITLE SRC KINASE IN COMPLEX WITH INHIBITOR AP23464 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: P60-SRC, C-SRC, PP60C-SRC; COMPND 6 EC: 2.7.1.112; COMPND 7 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: SRC, SRC1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF-9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PFASTBAC KEYWDS SRC KINASE INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.DALGARNO,T.STEHLE,P.SCHELLING,S.NARULA,T.SAWYER REVDAT 3 23-AUG-23 2BDJ 1 REMARK REVDAT 2 24-FEB-09 2BDJ 1 VERSN REVDAT 1 24-OCT-06 2BDJ 0 JRNL AUTH D.DALGARNO,T.STEHLE,S.NARULA,P.SCHELLING, JRNL AUTH 2 M.R.VAN SCHRAVENDIJK,S.ADAMS,L.ANDRADE,J.KEATS,M.RAM,L.JIN, JRNL AUTH 3 T.GROSSMAN,I.MACNEIL,C.METCALF III,W.SHAKESPEARE,Y.WANG, JRNL AUTH 4 T.KEENAN,R.SUNDARAMOORTHI,R.BOHACEK,M.WEIGELE,T.SAWYER JRNL TITL STRUCTURAL BASIS OF SRC TYROSINE KINASE INHIBITION WITH A JRNL TITL 2 NEW CLASS OF POTENT AND SELECTIVE TRISUBSTITUTED JRNL TITL 3 PURINE-BASED COMPOUNDS. JRNL REF CHEM.BIOL.DRUG DES. V. 67 46 2006 JRNL REFN ISSN 1747-0277 JRNL PMID 16492148 JRNL DOI 10.1111/J.1747-0285.2005.00316.X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 10% OF DATA REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 980 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 : 2048 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 161 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 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 2BDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000034968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.3 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 1FMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 200MM NH4NO3, PH 6.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.30000 REMARK 290 SMTRY3 2 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 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 LEU A 255 REMARK 465 ALA A 256 REMARK 465 ASP A 413 REMARK 465 ASN A 414 REMARK 465 GLU A 415 REMARK 465 TYR A 416 REMARK 465 THR A 417 REMARK 465 ALA A 418 REMARK 465 ARG A 419 REMARK 465 GLN A 420 REMARK 465 GLY A 421 REMARK 465 ALA A 422 REMARK 465 LYS A 423 REMARK 465 SER A 522 REMARK 465 THR A 523 REMARK 465 GLU A 524 REMARK 465 PRO A 525 REMARK 465 GLN A 526 REMARK 465 TYR A 527 REMARK 465 GLN A 528 REMARK 465 PRO A 529 REMARK 465 GLY A 530 REMARK 465 GLU A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 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 PRO A 488 C - N - CA ANGL. DEV. = 9.1 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 ASP A 258 -166.32 -163.92 REMARK 500 GLU A 270 -67.62 -127.55 REMARK 500 PHE A 278 70.69 -101.18 REMARK 500 PRO A 299 -15.69 -39.30 REMARK 500 THR A 301 -34.26 -28.02 REMARK 500 ARG A 385 -9.32 81.79 REMARK 500 ASN A 397 33.35 74.61 REMARK 500 ASP A 404 77.00 63.14 REMARK 500 ASN A 468 -77.59 -45.68 REMARK 500 GLU A 486 -13.74 77.95 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 HET A 800 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BDF RELATED DB: PDB REMARK 900 RELATED COMPLEX DBREF 2BDJ A 255 533 UNP P12931 SRC_HUMAN 257 535 SEQRES 1 A 279 LEU ALA LYS ASP ALA TRP GLU ILE PRO ARG GLU SER LEU SEQRES 2 A 279 ARG LEU GLU VAL LYS LEU GLY GLN GLY CYS PHE GLY GLU SEQRES 3 A 279 VAL TRP MET GLY THR TRP ASN GLY THR THR ARG VAL ALA SEQRES 4 A 279 ILE LYS THR LEU LYS PRO GLY THR MET SER PRO GLU ALA SEQRES 5 A 279 PHE LEU GLN GLU ALA GLN VAL MET LYS LYS LEU ARG HIS SEQRES 6 A 279 GLU LYS LEU VAL GLN LEU TYR ALA VAL VAL SER GLU GLU SEQRES 7 A 279 PRO ILE TYR ILE VAL THR GLU TYR MET SER LYS GLY SER SEQRES 8 A 279 LEU LEU ASP PHE LEU LYS GLY GLU THR GLY LYS TYR LEU SEQRES 9 A 279 ARG LEU PRO GLN LEU VAL ASP MET ALA ALA GLN ILE ALA SEQRES 10 A 279 SER GLY MET ALA TYR VAL GLU ARG MET ASN TYR VAL HIS SEQRES 11 A 279 ARG ASP LEU ARG ALA ALA ASN ILE LEU VAL GLY GLU ASN SEQRES 12 A 279 LEU VAL CYS LYS VAL ALA ASP PHE GLY LEU ALA ARG LEU SEQRES 13 A 279 ILE GLU ASP ASN GLU TYR THR ALA ARG GLN GLY ALA LYS SEQRES 14 A 279 PHE PRO ILE LYS TRP THR ALA PRO GLU ALA ALA LEU TYR SEQRES 15 A 279 GLY ARG PHE THR ILE LYS SER ASP VAL TRP SER PHE GLY SEQRES 16 A 279 ILE LEU LEU THR GLU LEU THR THR LYS GLY ARG VAL PRO SEQRES 17 A 279 TYR PRO GLY MET VAL ASN ARG GLU VAL LEU ASP GLN VAL SEQRES 18 A 279 GLU ARG GLY TYR ARG MET PRO CYS PRO PRO GLU CYS PRO SEQRES 19 A 279 GLU SER LEU HIS ASP LEU MET CYS GLN CYS TRP ARG LYS SEQRES 20 A 279 GLU PRO GLU GLU ARG PRO THR PHE GLU TYR LEU GLN ALA SEQRES 21 A 279 PHE LEU GLU ASP TYR PHE THR SER THR GLU PRO GLN TYR SEQRES 22 A 279 GLN PRO GLY GLU ASN LEU HET HET A 800 34 HETNAM HET 3-[2-(2-CYCLOPENTYL-6-{[4-(DIMETHYLPHOSPHORYL) HETNAM 2 HET PHENYL]AMINO}-9H-PURIN-9-YL)ETHYL]PHENOL FORMUL 2 HET C26 H30 N5 O2 P FORMUL 3 HOH *161(H2 O) HELIX 1 1 PRO A 263 GLU A 265 5 3 HELIX 2 2 SER A 303 LEU A 317 1 15 HELIX 3 3 LEU A 346 GLY A 352 1 7 HELIX 4 4 GLY A 352 TYR A 357 1 6 HELIX 5 5 ARG A 359 MET A 380 1 22 HELIX 6 6 ARG A 388 ALA A 390 5 3 HELIX 7 7 ALA A 430 GLY A 437 1 8 HELIX 8 8 THR A 440 THR A 457 1 18 HELIX 9 9 VAL A 467 ARG A 477 1 11 HELIX 10 10 PRO A 488 TRP A 499 1 12 HELIX 11 11 GLU A 502 ARG A 506 5 5 HELIX 12 12 THR A 508 TYR A 519 1 12 SHEET 1 A 5 LEU A 267 GLY A 274 0 SHEET 2 A 5 GLU A 280 TRP A 286 -1 O MET A 283 N GLU A 270 SHEET 3 A 5 THR A 290 THR A 296 -1 O THR A 290 N TRP A 286 SHEET 4 A 5 TYR A 335 THR A 338 -1 O THR A 338 N ALA A 293 SHEET 5 A 5 LEU A 325 VAL A 329 -1 N TYR A 326 O VAL A 337 SHEET 1 B 3 GLY A 344 SER A 345 0 SHEET 2 B 3 ILE A 392 VAL A 394 -1 O VAL A 394 N GLY A 344 SHEET 3 B 3 CYS A 400 VAL A 402 -1 O LYS A 401 N LEU A 393 SHEET 1 C 2 TYR A 382 VAL A 383 0 SHEET 2 C 2 ARG A 409 LEU A 410 -1 O ARG A 409 N VAL A 383 CISPEP 1 GLU A 332 PRO A 333 0 0.29 SITE 1 AC1 16 HOH A 45 LEU A 273 GLY A 274 VAL A 281 SITE 2 AC1 16 ALA A 293 LYS A 295 GLU A 310 ILE A 336 SITE 3 AC1 16 THR A 338 GLU A 339 TYR A 340 MET A 341 SITE 4 AC1 16 SER A 342 GLY A 344 LEU A 393 ASP A 404 CRYST1 42.100 54.600 69.000 90.00 99.97 90.00 P 1 21 1 2 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 0.004175 0.00000 SCALE2 0.000000 0.018315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014715 0.00000