HEADER TRANSFERASE 01-APR-07 2PE2 TITLE CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 TITLE 2 (PDK1) 3-{5-[2-OXO-5-UREIDO-1,2-DIHYDRO-INDOL-(3Z)-YLIDENEMETHYL]-1H- TITLE 3 PYRROL-3-YL}-N-(2-PIPERIDIN-1-YL-ETHYL)-BENZAMIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: HPDK1; COMPND 6 EC: 2.7.11.1; 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: PDPK1, PDK1; SOURCE 6 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF-21 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PBLUEBAC4.5; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDK1-CAT/PBB4.5 KEYWDS PROTEIN INHIBITOR COMPLEX, SERINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.WHITLOW,M.ADLER REVDAT 4 13-JUL-11 2PE2 1 VERSN REVDAT 3 24-FEB-09 2PE2 1 VERSN REVDAT 2 17-JUL-07 2PE2 1 JRNL REVDAT 1 19-JUN-07 2PE2 0 JRNL AUTH I.ISLAM,G.BROWN,J.BRYANT,P.HRVATIN,M.J.KOCHANNY, JRNL AUTH 2 G.B.PHILLIPS,S.YUAN,M.ADLER,M.WHITLOW,D.LENTZ,M.A.POLOKOFF, JRNL AUTH 3 J.WU,J.SHEN,J.WALTERS,E.HO,B.SUBRAMANYAM,D.ZHU,R.I.FELDMAN, JRNL AUTH 4 D.O.ARNAIZ JRNL TITL INDOLINONE BASED PHOSPHOINOSITIDE-DEPENDENT KINASE-1 (PDK1) JRNL TITL 2 INHIBITORS. PART 2: OPTIMIZATION OF BX-517. JRNL REF BIOORG.MED.CHEM.LETT. V. 17 3819 2007 JRNL REFN ISSN 0960-894X JRNL PMID 17544272 JRNL DOI 10.1016/J.BMCL.2007.05.060 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.ISLAM,J.BRYANT,Y.-L.CHOU,M.J.KOCHANNY,W.LEE,G.B.PHILLIPS, REMARK 1 AUTH 2 H.YU,M.ADLER,M.WHITLOW,E.HO,D.LENTZ,M.A.POLOKOFF, REMARK 1 AUTH 3 B.SUBRAMANYAM,J.M.WU,D.ZHU,R.I.FELDMAN,D.O.ARNAIZ REMARK 1 TITL INDOLINONE BASED PHHOSPHOINOSITIDE-DEPENDENT KINASE-1 (PDK1) REMARK 1 TITL 2 INHIBITORS- PART 1: DESIGN, SYNTHESIS AND BILLOGICAL REMARK 1 TITL 3 ACTIVITY REMARK 1 REF TO BE PUBLISHED 2007 REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH R.I.FELDMAN,J.M.WU,M.A.POLOKOFF,M.J.KOCHANNY,H.DINTER,D.ZHU, REMARK 1 AUTH 2 S.L.BIROC,B.ALICKE,J.BRYANT,S.YUAN,B.O.BUCKMAN,D.LENTZ, REMARK 1 AUTH 3 M.FERRER,M.WHITLOW,M.ADLER,S.FINSTER,Z.CHANG,D.O.ARNAIZ REMARK 1 TITL NOVEL SMALL MOLECULE INHIBITORS OF REMARK 1 TITL 2 3-PHOSPHOINOSITIDE-DEPENDENT KINASE-1. REMARK 1 REF J.BIOL.CHEM. V. 280 19867 2005 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.M.BIONDI,D.KOMANDER,C.C.THOMAS,J.M.LIZCANO,M.DEAK, REMARK 1 AUTH 2 D.R.ALESSI,D.M.F.VAN AALTEN REMARK 1 TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 REMARK 1 TITL 2 CATALYTIC DOMAIN DEFINES THE REGULATORY PHOSPHOPEPTIDE REMARK 1 TITL 3 DOCKING SITE. REMARK 1 REF EMBO J. V. 21 4219 2002 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 137258.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 20101 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 843 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2010 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2000 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 950 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0070 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22905 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2581 REMARK 3 BIN R VALUE (WORKING SET) : 0.2419 REMARK 3 BIN FREE R VALUE : 0.3023 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2255 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : -0.47000 REMARK 3 B12 (A**2) : 2.96000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.64 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.440 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.660 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 71.76 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : WATER_REP.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : SPH.PAR REMARK 3 PARAMETER FILE 5 : 464.PAR REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : SPH.TOP REMARK 3 TOPOLOGY FILE 5 : 464.TOP REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PE2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-07. REMARK 100 THE RCSB ID CODE IS RCSB042273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22919 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.280 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06650 REMARK 200 FOR THE DATA SET : 9.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.16 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35120 REMARK 200 FOR SHELL : 1.720 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER PLUS REMARK 200 REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR, XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, EDTA, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 31.59067 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 15.79533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.79533 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 31.59067 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.97667 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 SER A 231 REMARK 465 PRO A 232 REMARK 465 GLU A 233 REMARK 465 SER A 234 REMARK 465 LYS A 235 REMARK 465 GLN A 236 REMARK 465 ALA A 237 REMARK 465 ARG A 238 REMARK 465 ALA A 239 REMARK 465 ASN A 240 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 ARG A 75 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 ASP A 151 -159.95 -111.93 REMARK 500 ARG A 204 -8.69 75.80 REMARK 500 ASP A 205 41.37 -145.91 REMARK 500 ASP A 223 72.01 78.63 REMARK 500 THR A 255 -60.28 -104.73 REMARK 500 PHE A 305 122.19 -34.57 REMARK 500 ASN A 349 42.45 -141.80 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 SO4 A 599 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 464 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 609 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z5M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N1-[3-[[5-BROMO-2-[[3-[(1- REMARK 900 PYRROLIDINYLCARBONYL)AMINO]PHENYL]AMINO]-4-PYRIMIDINYL] REMARK 900 AMINO]PROPYL]-2,2-DIMETHYLPROPANEDIAMIDE COMPLEXED WITH REMARK 900 HUMAN PDK1 REMARK 900 RELATED ID: 1OKY RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH REMARK 900 STAUROSPORINE REMARK 900 RELATED ID: 1OKZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01 REMARK 900 RELATED ID: 1UU3 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH REMARK 900 LY333531 REMARK 900 RELATED ID: 1UU7 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2 REMARK 900 RELATED ID: 1UU8 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1 REMARK 900 RELATED ID: 1UU9 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 REMARK 900 RELATED ID: 1UVR RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 REMARK 900 RELATED ID: 1H1W RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 REMARK 900 CATALYTIC DOMAIN REMARK 900 RELATED ID: 2PE0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT REMARK 900 PROTEIN KINASE 1 (PDK1) 5-HYDROXY-3-[1-(1H-PYRROL-2-YL)-ETH REMARK 900 -(Z)-YLIDENE]-1,3-DIHYDRO- INDOL-2-ONE COMPLEX REMARK 900 RELATED ID: 2PE1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT REMARK 900 PROTEIN KINASE 1 (PDK1) {2-OXO-3-[1-(1H-PYRROL-2-YL)-ETH- REMARK 900 (Z)-YLIDENE]-2,3-DIHYDRO-1H- INDOL-5-YL}-UREA {BX-517} REMARK 900 COMPLEX DBREF 2PE2 A 74 359 UNP O15530 PDPK1_HUMAN 74 359 SEQADV 2PE2 SEP A 241 UNP O15530 SER 241 MODIFIED RESIDUE SEQRES 1 A 286 PRO ARG LYS LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS SEQRES 2 A 286 ILE LEU GLY GLU GLY SER PHE SER THR VAL VAL LEU ALA SEQRES 3 A 286 ARG GLU LEU ALA THR SER ARG GLU TYR ALA ILE LYS ILE SEQRES 4 A 286 LEU GLU LYS ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO SEQRES 5 A 286 TYR VAL THR ARG GLU ARG ASP VAL MET SER ARG LEU ASP SEQRES 6 A 286 HIS PRO PHE PHE VAL LYS LEU TYR PHE THR PHE GLN ASP SEQRES 7 A 286 ASP GLU LYS LEU TYR PHE GLY LEU SER TYR ALA LYS ASN SEQRES 8 A 286 GLY GLU LEU LEU LYS TYR ILE ARG LYS ILE GLY SER PHE SEQRES 9 A 286 ASP GLU THR CYS THR ARG PHE TYR THR ALA GLU ILE VAL SEQRES 10 A 286 SER ALA LEU GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS SEQRES 11 A 286 ARG ASP LEU LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP SEQRES 12 A 286 MET HIS ILE GLN ILE THR ASP PHE GLY THR ALA LYS VAL SEQRES 13 A 286 LEU SER PRO GLU SER LYS GLN ALA ARG ALA ASN SEP PHE SEQRES 14 A 286 VAL GLY THR ALA GLN TYR VAL SER PRO GLU LEU LEU THR SEQRES 15 A 286 GLU LYS SER ALA CYS LYS SER SER ASP LEU TRP ALA LEU SEQRES 16 A 286 GLY CYS ILE ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO SEQRES 17 A 286 PHE ARG ALA GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE SEQRES 18 A 286 ILE LYS LEU GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO SEQRES 19 A 286 LYS ALA ARG ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP SEQRES 20 A 286 ALA THR LYS ARG LEU GLY CYS GLU GLU MET GLU GLY TYR SEQRES 21 A 286 GLY PRO LEU LYS ALA HIS PRO PHE PHE GLU SER VAL THR SEQRES 22 A 286 TRP GLU ASN LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 2PE2 SEP A 241 SER PHOSPHOSERINE HET SEP A 241 10 HET SO4 A 599 5 HET SO4 A 600 5 HET SO4 A 601 5 HET 464 A 501 37 HET GOL A 602 6 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET GOL A 608 6 HET GOL A 609 6 HETNAM SEP PHOSPHOSERINE HETNAM SO4 SULFATE ION HETNAM 464 3-[5-({5-[(AMINOCARBONYL)AMINO]-2-OXO-2H-INDOL-3- HETNAM 2 464 YL}METHYL)-1H-PYRROL-3-YL]-N-(2-PIPERIDIN-1-YLETHYL) HETNAM 3 464 BENZAMIDE HETNAM GOL GLYCEROL HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 464 C28 H30 N6 O3 FORMUL 6 GOL 8(C3 H8 O3) FORMUL 14 HOH *161(H2 O) HELIX 1 1 ARG A 78 GLU A 80 5 3 HELIX 2 2 LYS A 115 GLU A 121 1 7 HELIX 3 3 LYS A 123 LEU A 137 1 15 HELIX 4 4 GLU A 166 GLY A 175 1 10 HELIX 5 5 ASP A 178 LYS A 199 1 22 HELIX 6 6 THR A 245 VAL A 249 5 5 HELIX 7 7 SER A 250 GLU A 256 1 7 HELIX 8 8 CYS A 260 GLY A 278 1 19 HELIX 9 9 ASN A 286 LEU A 297 1 12 HELIX 10 10 PHE A 306 LEU A 317 1 12 HELIX 11 11 ASP A 320 ARG A 324 5 5 HELIX 12 12 CYS A 327 GLU A 331 5 5 HELIX 13 13 GLY A 332 ALA A 338 1 7 HELIX 14 14 HIS A 339 GLU A 343 5 5 HELIX 15 15 THR A 346 GLN A 353 5 8 SHEET 1 A 5 PHE A 82 GLU A 90 0 SHEET 2 A 5 THR A 95 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 A 5 GLU A 107 GLU A 114 -1 O ILE A 112 N THR A 95 SHEET 4 A 5 LYS A 154 LEU A 159 -1 O LEU A 155 N LEU A 113 SHEET 5 A 5 LEU A 145 GLN A 150 -1 N PHE A 147 O GLY A 158 SHEET 1 B 2 ILE A 201 ILE A 202 0 SHEET 2 B 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 SHEET 1 C 2 ILE A 211 LEU A 213 0 SHEET 2 C 2 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 SITE 1 AC1 4 ARG A 106 PRO A 140 HIS A 351 GOL A 609 SITE 1 AC2 6 LYS A 76 ARG A 131 THR A 148 PHE A 149 SITE 2 AC2 6 GLN A 150 HOH A 781 SITE 1 AC3 3 ARG A 75 ARG A 136 LYS A 199 SITE 1 AC4 14 ALA A 109 LYS A 111 SER A 160 TYR A 161 SITE 2 AC4 14 ALA A 162 LYS A 163 ASN A 164 GLY A 165 SITE 3 AC4 14 LYS A 169 TYR A 170 LEU A 212 THR A 222 SITE 4 AC4 14 ASP A 223 GOL A 602 SITE 1 AC5 9 GLY A 89 GLU A 90 GLY A 91 SER A 94 SITE 2 AC5 9 VAL A 96 464 A 501 GOL A 608 HOH A 772 SITE 3 AC5 9 HOH A 934 SITE 1 AC6 5 PHE A 84 GLU A 194 GLY A 334 LYS A 337 SITE 2 AC6 5 HOH A 832 SITE 1 AC7 10 ALA A 103 THR A 104 SER A 105 HIS A 139 SITE 2 AC7 10 TRP A 347 GLU A 348 ASN A 349 LEU A 350 SITE 3 AC7 10 HIS A 351 HOH A 820 SITE 1 AC8 4 VAL A 318 LEU A 319 ASP A 320 LYS A 323 SITE 1 AC9 6 PHE A 84 LYS A 154 TYR A 156 GLU A 328 SITE 2 AC9 6 GLU A 331 GLY A 332 SITE 1 BC1 4 LYS A 111 TYR A 126 GLU A 130 GOL A 608 SITE 1 BC2 5 GLY A 91 SER A 92 PHE A 93 GOL A 602 SITE 2 BC2 5 GOL A 607 SITE 1 BC3 7 ARG A 106 GLU A 107 TYR A 108 TYR A 146 SITE 2 BC3 7 SER A 160 TYR A 161 SO4 A 599 CRYST1 123.223 123.223 47.386 90.00 90.00 120.00 P 32 2 1 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 0.008115 0.004685 0.000000 0.00000 SCALE2 0.000000 0.009371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021103 0.00000