PDB Short entry for 3RWP HEADER TRANSFERASE/TRANSFERASE INHIBITOR 09-MAY-11 3RWP TITLE DISCOVERY OF A NOVEL, POTENT AND SELECTIVE INHIBITOR OF 3- TITLE 2 PHOSPHOINOSITIDE DEPENDENT KINASE (PDK1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 51-359; 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: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS KINASE DOMAIN, TRANSFERASE, PHOSPHOSERINE: SEP, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.E.GREASLEY,M.HICKEY,R.-A.FERRE,M.KRAUSS,C.CRONIN REVDAT 3 08-NOV-17 3RWP 1 REMARK REVDAT 2 28-DEC-11 3RWP 1 JRNL REVDAT 1 16-NOV-11 3RWP 0 JRNL AUTH S.T.MURPHY,G.ALTON,S.BAILEY,S.M.BAXI,B.J.BURKE,T.A.CHAPPIE, JRNL AUTH 2 J.ERMOLIEFF,R.FERRE,S.GREASLEY,M.HICKEY,J.HUMPHREY, JRNL AUTH 3 N.KABLAOUI,J.KATH,S.KAZMIRSKI,M.KRAUS,S.KUPCHINSKY,J.LI, JRNL AUTH 4 L.LINGARDO,M.A.MARX,D.RICHTER,S.P.TANIS,K.TRAN,W.VERNIER, JRNL AUTH 5 Z.XIE,M.J.YIN,X.H.YU JRNL TITL DISCOVERY OF NOVEL, POTENT, AND SELECTIVE INHIBITORS OF JRNL TITL 2 3-PHOSPHOINOSITIDE-DEPENDENT KINASE (PDK1). JRNL REF J.MED.CHEM. V. 54 8490 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 22040023 JRNL DOI 10.1021/JM201019K REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 30059 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1600 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2202 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2269 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.30000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.637 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2416 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3263 ; 2.226 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.604 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;33.720 ;23.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;14.095 ;15.035 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.692 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 342 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1829 ; 0.012 ; 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): 1393 ; 1.506 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2255 ; 2.571 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1023 ; 3.833 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1008 ; 5.990 ; 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: NULL REMARK 4 REMARK 4 3RWP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.0 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) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31671 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 10MM EDTA, 5 REMARK 280 -10% GLYCEROL, 0.1M HEPES, PH 7.0., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 31.67000 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 15.83500 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 15.83500 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 31.67000 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 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: 8610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -224.0 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 47.50500 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 ALA A 49 REMARK 465 LEU A 50 REMARK 465 MET A 51 REMARK 465 ASP A 52 REMARK 465 GLY A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 ALA A 56 REMARK 465 GLU A 57 REMARK 465 PRO A 58 REMARK 465 ARG A 59 REMARK 465 PRO A 60 REMARK 465 GLY A 61 REMARK 465 ALA A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 LEU A 65 REMARK 465 GLN A 66 REMARK 465 HIS A 67 REMARK 465 ALA A 68 REMARK 465 GLN A 69 REMARK 465 PRO A 70 REMARK 465 PRO A 71 REMARK 465 PRO A 72 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 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 141 CE1 PHE A 141 CZ 0.140 REMARK 500 SER A 160 CB SER A 160 OG -0.096 REMARK 500 SER A 262 CB SER A 262 OG -0.080 REMARK 500 GLU A 348 CB GLU A 348 CG 0.127 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 151 -161.01 -109.67 REMARK 500 ARG A 204 -7.14 75.52 REMARK 500 ASP A 205 44.49 -145.30 REMARK 500 ASP A 223 68.90 73.21 REMARK 500 GLU A 256 22.54 -162.53 REMARK 500 LYS A 257 59.97 26.35 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 GOL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ABQ A 360 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SC1 RELATED DB: PDB REMARK 900 NOVEL ISOQUINOLONE PDK1 INHIBITORS DISCOVERED THROUGH FRAGMENT- REMARK 900 BASED LEAD DISCOVERY REMARK 900 RELATED ID: 3RWQ RELATED DB: PDB REMARK 900 DISCOVERY OF A NOVEL, POTENT AND SELECTIVE INHIBITOR OF 3- REMARK 900 PHOSPHOINOSITIDE DEPENDENT KINASE (PDK1) DBREF 3RWP A 51 359 UNP O15530 PDPK1_HUMAN 51 359 SEQADV 3RWP ALA A 49 UNP O15530 EXPRESSION TAG SEQADV 3RWP LEU A 50 UNP O15530 EXPRESSION TAG SEQRES 1 A 311 ALA LEU MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY SEQRES 2 A 311 ALA GLY SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO SEQRES 3 A 311 ARG LYS LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE SEQRES 4 A 311 LEU GLY GLU GLY SER PHE SER THR VAL VAL LEU ALA ARG SEQRES 5 A 311 GLU LEU ALA THR SER ARG GLU TYR ALA ILE LYS ILE LEU SEQRES 6 A 311 GLU LYS ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR SEQRES 7 A 311 VAL THR ARG GLU ARG ASP VAL MET SER ARG LEU ASP HIS SEQRES 8 A 311 PRO PHE PHE VAL LYS LEU TYR PHE THR PHE GLN ASP ASP SEQRES 9 A 311 GLU LYS LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY SEQRES 10 A 311 GLU LEU LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP SEQRES 11 A 311 GLU THR CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER SEQRES 12 A 311 ALA LEU GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG SEQRES 13 A 311 ASP LEU LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET SEQRES 14 A 311 HIS ILE GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SEQRES 15 A 311 SER PRO GLU SER LYS GLN ALA ARG ALA ASN SEP PHE VAL SEQRES 16 A 311 GLY THR ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU SEQRES 17 A 311 LYS SER ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY SEQRES 18 A 311 CYS ILE ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE SEQRES 19 A 311 ARG ALA GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE SEQRES 20 A 311 LYS LEU GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS SEQRES 21 A 311 ALA ARG ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA SEQRES 22 A 311 THR LYS ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY SEQRES 23 A 311 PRO LEU LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP SEQRES 24 A 311 GLU ASN LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 3RWP SEP A 241 SER PHOSPHOSERINE HET SEP A 241 10 HET GOL A 901 6 HET GOL A 902 6 HET GOL A 903 6 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET SO4 A 907 5 HET SO4 A 908 5 HET SO4 A 909 5 HET GOL A 910 6 HET ABQ A 360 34 HETNAM SEP PHOSPHOSERINE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM ABQ [4-AMINO-7-(PROPAN-2-YL)-7H-PYRROLO[2,3-D]PYRIMIDIN-5- HETNAM 2 ABQ YL](6-{[(3S,4R)-4-(4-FLUOROPHENYL)TETRAHYDROFURAN-3- HETNAM 3 ABQ YL]AMINO}PYRAZIN-2-YL)METHANONE HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 GOL 4(C3 H8 O3) FORMUL 5 SO4 6(O4 S 2-) FORMUL 12 ABQ C24 H24 F N7 O2 FORMUL 13 HOH *205(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 LEU A 167 GLY A 175 1 9 HELIX 5 5 ASP A 178 LYS A 199 1 22 HELIX 6 6 LYS A 207 GLU A 209 5 3 HELIX 7 7 THR A 245 VAL A 249 5 5 HELIX 8 8 SER A 250 LYS A 257 1 8 HELIX 9 9 CYS A 260 GLY A 278 1 19 HELIX 10 10 ASN A 286 LYS A 296 1 11 HELIX 11 11 PHE A 306 LYS A 315 1 10 HELIX 12 12 ASP A 320 ARG A 324 5 5 HELIX 13 13 CYS A 327 GLU A 331 5 5 HELIX 14 14 GLY A 332 ALA A 338 1 7 HELIX 15 15 HIS A 339 GLU A 343 5 5 HELIX 16 16 ASN A 349 GLN A 353 5 5 SHEET 1 A 5 PHE A 82 GLU A 90 0 SHEET 2 A 5 SER A 94 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 SER A 160 -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 3 GLY A 165 GLU A 166 0 SHEET 2 B 3 ILE A 211 LEU A 213 -1 O LEU A 213 N GLY A 165 SHEET 3 B 3 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 C 2 ILE A 201 ILE A 202 0 SHEET 2 C 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 CISPEP 1 LEU A 358 THR A 359 0 25.94 SITE 1 AC1 8 ARG A 106 GLU A 107 SER A 160 TYR A 161 SITE 2 AC1 8 HOH A 434 SO4 A 904 SO4 A 907 SO4 A 908 SITE 1 AC2 9 ALA A 103 THR A 104 HIS A 139 SER A 191 SITE 2 AC2 9 TRP A 347 GLU A 348 ASN A 349 LEU A 350 SITE 3 AC2 9 HIS A 351 SITE 1 AC3 7 PRO A 79 PHE A 84 LYS A 154 TYR A 156 SITE 2 AC3 7 GLU A 328 GLU A 331 GLY A 332 SITE 1 AC4 6 ARG A 106 HIS A 351 HOH A 398 HOH A 453 SITE 2 AC4 6 GOL A 901 SO4 A 908 SITE 1 AC5 7 LYS A 76 ARG A 131 THR A 148 PHE A 149 SITE 2 AC5 7 GLN A 150 HOH A 386 HOH A 414 SITE 1 AC6 4 LYS A 144 TYR A 146 HOH A 453 SO4 A 907 SITE 1 AC7 7 TYR A 146 SER A 160 GLN A 220 HOH A 431 SITE 2 AC7 7 HOH A 505 GOL A 901 SO4 A 906 SITE 1 AC8 7 ARG A 106 GLU A 107 HIS A 351 GLN A 352 SITE 2 AC8 7 HOH A 434 GOL A 901 SO4 A 904 SITE 1 AC9 4 GLN A 73 ARG A 75 ARG A 136 LYS A 199 SITE 1 BC1 8 HOH A 15 GLY A 91 SER A 92 PHE A 93 SITE 2 BC1 8 ABQ A 360 HOH A 377 HOH A 423 HOH A 424 SITE 1 BC2 20 HOH A 1 HOH A 3 LEU A 88 GLY A 89 SITE 2 BC2 20 GLU A 90 GLY A 91 SER A 94 THR A 95 SITE 3 BC2 20 VAL A 96 ALA A 109 LYS A 111 LEU A 159 SITE 4 BC2 20 SER A 160 ALA A 162 GLU A 166 GLU A 209 SITE 5 BC2 20 LEU A 212 THR A 222 ASP A 223 GOL A 910 CRYST1 122.982 122.982 47.505 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 0.008131 0.004695 0.000000 0.00000 SCALE2 0.000000 0.009389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021050 0.00000