HEADER TRANSFERASE 18-OCT-16 5M4P TITLE APPLICATION OF OFF-RATE SCREENING IN THE IDENTIFICATION OF NOVEL PAN- TITLE 2 ISOFORM INHIBITORS OF PYRUVATE DEHYDROGENASE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE COMPND 3 ISOZYME 2, MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2,PDKII; COMPND 6 EC: 2.7.11.2; 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: PDK2, PDHK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS OFF-RATE SCREENING, PDHK, HSP90, SPR, KINASE INHIBITORS, FRAGMENT KEYWDS 2 SCREENING, CANCER, PDK1, PDK2, PDK3, PDK4, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.M.BAKER,P.BROUGH,A.SURGENOR REVDAT 4 17-JAN-24 5M4P 1 REMARK REVDAT 3 24-OCT-18 5M4P 1 REMARK LINK REVDAT 2 05-APR-17 5M4P 1 JRNL REVDAT 1 22-FEB-17 5M4P 0 JRNL AUTH P.A.BROUGH,L.BAKER,S.BEDFORD,K.BROWN,S.CHAVDA,V.CHELL, JRNL AUTH 2 J.D'ALESSANDRO,N.G.DAVIES,B.DAVIS,L.LE STRAT,A.T.MACIAS, JRNL AUTH 3 D.MADDOX,P.C.MAHON,A.J.MASSEY,N.MATASSOVA,S.MCKENNA, JRNL AUTH 4 J.W.MEISSNER,J.D.MOORE,J.B.MURRAY,C.J.NORTHFIELD,C.PARRY, JRNL AUTH 5 R.PARSONS,S.D.ROUGHLEY,T.SHAW,H.SIMMONITE,S.STOKES, JRNL AUTH 6 A.SURGENOR,E.STEFANIAK,A.ROBERTSON,Y.WANG,P.WEBB, JRNL AUTH 7 N.WHITEHEAD,M.WOOD JRNL TITL APPLICATION OF OFF-RATE SCREENING IN THE IDENTIFICATION OF JRNL TITL 2 NOVEL PAN-ISOFORM INHIBITORS OF PYRUVATE DEHYDROGENASE JRNL TITL 3 KINASE. JRNL REF J. MED. CHEM. V. 60 2271 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28199108 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01478 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 24244 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1300 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1752 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2749 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.94000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -3.04000 REMARK 3 B12 (A**2) : 0.47000 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): 0.227 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2880 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2734 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3897 ; 1.858 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6243 ; 1.161 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 5.946 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;35.049 ;24.063 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;18.695 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.898 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3183 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 637 ; 0.002 ; 0.020 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): 1368 ; 4.270 ; 5.225 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1367 ; 4.227 ; 5.223 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1703 ; 6.137 ; 7.797 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1704 ; 6.136 ; 7.800 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1512 ; 4.904 ; 5.726 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1513 ; 4.902 ; 5.726 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2195 ; 7.484 ; 8.389 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 12036 ;10.880 ;49.446 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11997 ;10.884 ;49.447 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 5M4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5412 REMARK 200 MONOCHROMATOR : CU FILTER REMARK 200 OPTICS : OSMIC BLUE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25546 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.650 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.53 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 2BU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.8 0.125 M REMARK 280 MAGNESIUM CHLORIDE 6% ISOPROPANOL, VAPOR DIFFUSION, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.17167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.34333 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.17167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.34333 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 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 MET A -8 REMARK 465 ARG A -7 REMARK 465 TRP A -6 REMARK 465 VAL A -5 REMARK 465 TRP A -4 REMARK 465 ALA A -3 REMARK 465 LEU A -2 REMARK 465 LEU A -1 REMARK 465 LYS A 0 REMARK 465 ASN A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 SER A 34 REMARK 465 GLY A 170 REMARK 465 SER A 171 REMARK 465 THR A 172 REMARK 465 ASN A 173 REMARK 465 PRO A 174 REMARK 465 ALA A 175 REMARK 465 HIS A 176 REMARK 465 THR A 305 REMARK 465 PRO A 306 REMARK 465 GLN A 307 REMARK 465 PRO A 308 REMARK 465 GLY A 309 REMARK 465 THR A 310 REMARK 465 GLY A 311 REMARK 465 GLY A 312 REMARK 465 THR A 313 REMARK 465 PRO A 314 REMARK 465 ASN A 367 REMARK 465 LYS A 368 REMARK 465 SER A 369 REMARK 465 ALA A 370 REMARK 465 TRP A 371 REMARK 465 ARG A 372 REMARK 465 HIS A 373 REMARK 465 TYR A 374 REMARK 465 GLN A 375 REMARK 465 THR A 376 REMARK 465 ILE A 377 REMARK 465 GLN A 378 REMARK 465 GLU A 379 REMARK 465 ALA A 380 REMARK 465 GLY A 381 REMARK 465 ASP A 382 REMARK 465 TRP A 383 REMARK 465 CYS A 384 REMARK 465 VAL A 385 REMARK 465 PRO A 386 REMARK 465 SER A 387 REMARK 465 THR A 388 REMARK 465 GLU A 389 REMARK 465 PRO A 390 REMARK 465 LYS A 391 REMARK 465 ASN A 392 REMARK 465 THR A 393 REMARK 465 SER A 394 REMARK 465 THR A 395 REMARK 465 TYR A 396 REMARK 465 ARG A 397 REMARK 465 VAL A 398 REMARK 465 SER A 399 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 ASN A 35 CG OD1 ND2 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 C SER A 33 CB ASN A 35 1.58 REMARK 500 OD1 ASN A 61 NE2 GLN A 77 1.62 REMARK 500 ND2 ASN A 223 OE1 GLN A 226 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 131 OD2 ASP A 195 3654 1.68 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 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 158 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 283 NE - CZ - NH1 ANGL. DEV. = 3.4 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 ALA A 36 -24.50 81.43 REMARK 500 CYS A 37 48.46 -82.61 REMARK 500 PHE A 168 64.69 -107.94 REMARK 500 LYS A 178 -85.26 52.25 REMARK 500 SER A 224 -30.72 -34.83 REMARK 500 PHE A 332 43.86 -104.52 REMARK 500 PHE A 344 -76.02 -132.96 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 7FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TF3 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404 DBREF 5M4P A -8 399 UNP Q15119 PDK2_HUMAN 1 407 SEQADV 5M4P SER A 7 UNP Q15119 INSERTION SEQRES 1 A 408 MET ARG TRP VAL TRP ALA LEU LEU LYS ASN ALA SER LEU SEQRES 2 A 408 ALA GLY SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS SEQRES 3 A 408 PHE SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP SEQRES 4 A 408 PHE GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR SEQRES 5 A 408 PHE LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE SEQRES 6 A 408 MET LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER SEQRES 7 A 408 THR PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SEQRES 8 A 408 SER LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO SEQRES 9 A 408 GLU ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU SEQRES 10 A 408 VAL THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR SEQRES 11 A 408 MET ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY SEQRES 12 A 408 ASP ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU SEQRES 13 A 408 ASP ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU SEQRES 14 A 408 ILE ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN SEQRES 15 A 408 PRO ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN SEQRES 16 A 408 CYS ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET SEQRES 17 A 408 ALA LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO SEQRES 18 A 408 ASP LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS SEQRES 19 A 408 GLN PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR SEQRES 20 A 408 HIS MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA SEQRES 21 A 408 THR VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO SEQRES 22 A 408 ILE LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER SEQRES 23 A 408 ILE LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG SEQRES 24 A 408 LYS ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA SEQRES 25 A 408 PRO THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA SEQRES 26 A 408 GLY PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA SEQRES 27 A 408 LYS TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU SEQRES 28 A 408 GLY PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SEQRES 29 A 408 SER THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SEQRES 30 A 408 SER ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY SEQRES 31 A 408 ASP TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER SEQRES 32 A 408 THR TYR ARG VAL SER HET 7FE A 401 38 HET TF3 A 402 25 HET CL A 403 1 HET CL A 404 1 HETNAM 7FE ~{N}-[4-(2-CHLORANYL-5-METHYL-PYRIMIDIN-4-YL)PHENYL]-2, HETNAM 2 7FE 4-BIS(OXIDANYL)-~{N}-[[4-(PYRROLIDIN-1-YLMETHYL) HETNAM 3 7FE PHENYL]METHYL]BENZAMIDE HETNAM TF3 N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL) HETNAM 2 TF3 OXY]PHENYL} ACETAMIDE HETNAM CL CHLORIDE ION FORMUL 2 7FE C30 H29 CL N4 O3 FORMUL 3 TF3 C20 H25 CL N2 O2 FORMUL 4 CL 2(CL 1-) FORMUL 6 HOH *121(H2 O) HELIX 1 AA1 SER A 7 SER A 16 1 10 HELIX 2 AA2 SER A 24 GLY A 32 1 9 HELIX 3 AA3 CYS A 37 LEU A 62 1 26 HELIX 4 AA4 PRO A 64 SER A 69 1 6 HELIX 5 AA5 THR A 70 GLU A 89 1 20 HELIX 6 AA6 ASP A 97 HIS A 115 1 19 HELIX 7 AA7 ASP A 117 GLY A 134 1 18 HELIX 8 AA8 ASP A 136 PHE A 168 1 33 HELIX 9 AA9 VAL A 189 MET A 209 1 21 HELIX 10 AB1 VAL A 233 HIS A 256 1 24 HELIX 11 AB2 PRO A 288 SER A 297 5 10 HELIX 12 AB3 GLY A 321 PHE A 332 1 12 HELIX 13 AB4 LEU A 355 SER A 359 5 5 SHEET 1 AA1 2 ASP A 184 ASN A 188 0 SHEET 2 AA1 2 HIS A 229 TYR A 232 -1 O TYR A 232 N ASP A 184 SHEET 1 AA2 5 LEU A 214 ASN A 220 0 SHEET 2 AA2 5 ILE A 265 LEU A 271 1 O LEU A 271 N ILE A 219 SHEET 3 AA2 5 ASP A 275 SER A 281 -1 O SER A 281 N LYS A 266 SHEET 4 AA2 5 GLY A 345 LYS A 353 -1 O ALA A 348 N MET A 280 SHEET 5 AA2 5 ASP A 335 MET A 341 -1 N ASP A 335 O TYR A 351 SITE 1 AC1 12 LEU A 244 LYS A 246 ASN A 247 ARG A 250 SITE 2 AC1 12 ALA A 251 ASP A 282 GLY A 284 GLY A 286 SITE 3 AC1 12 VAL A 287 THR A 346 HOH A 518 HOH A 524 SITE 1 AC2 8 PRO A 64 ARG A 66 VAL A 67 VAL A 73 SITE 2 AC2 8 TYR A 129 ASN A 142 ILE A 143 LEU A 147 SITE 1 AC3 1 ARG A 362 SITE 1 AC4 1 LEU A 338 CRYST1 109.442 109.442 84.515 90.00 90.00 120.00 P 64 6 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 0.009137 0.005275 0.000000 0.00000 SCALE2 0.000000 0.010551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011832 0.00000