HEADER TRANSFERASE 23-APR-10 2XCK TITLE CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE CATALYTIC DOMAIN, RESIDUES 1-309; 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS PI3-KINASE SIGNALLING, TRANSFERASE, ATP-BINDING, SERINE/THREONINE- KEYWDS 2 PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ANGIOLINI,P.BANFI,E.CASALE,F.CASUSCELLI,C.FIORELLI,M.B.SACCARDO, AUTHOR 2 M.SILVAGNI,F.ZUCCOTTO REVDAT 3 16-OCT-24 2XCK 1 REMARK REVDAT 2 20-DEC-23 2XCK 1 REMARK LINK REVDAT 1 28-JUL-10 2XCK 0 JRNL AUTH M.ANGIOLINI,P.BANFI,E.CASALE,F.CASUSCELLI,C.FIORELLI, JRNL AUTH 2 M.B.SACCARDO,M.SILVAGNI,F.ZUCCOTTO JRNL TITL STRUCTURE-BASED OPTIMIZATION OF POTENT PDK1 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 4095 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20621725 JRNL DOI 10.1016/J.BMCL.2010.05.070 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17604 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 948 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) : 1288 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : 0.99000 REMARK 3 B33 (A**2) : -1.49000 REMARK 3 B12 (A**2) : 0.50000 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): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.743 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2386 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3217 ; 1.701 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 7.161 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;34.223 ;23.738 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;16.823 ;15.035 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;19.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1766 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1068 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1589 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 154 ; 0.191 ; 0.200 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): 55 ; 0.513 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.206 ; 0.200 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): 1430 ; 1.129 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2227 ; 1.989 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1106 ; 2.842 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 990 ; 4.283 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2XCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18571 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 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) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1H1W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS PH REMARK 280 8.5 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 31.49333 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 15.74667 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 15.74667 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 31.49333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.5 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 47.24000 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 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 GLN A 73 REMARK 465 PRO A 74 REMARK 465 ARG A 75 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 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 PHE A 93 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE A 242 CZ 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 CE MET A 134 O HOH A 2072 2.06 REMARK 500 OE2 GLU A 166 O HOH A 2043 2.18 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 S SO4 A 1369 O1 SO4 A 1369 4556 1.17 REMARK 500 O3 SO4 A 1369 O4 SO4 A 1369 4556 1.28 REMARK 500 O1 SO4 A 1369 O2 SO4 A 1369 4556 1.42 REMARK 500 O1 SO4 A 1369 O4 SO4 A 1369 4556 1.50 REMARK 500 O2 SO4 A 1369 O2 SO4 A 1369 4556 1.51 REMARK 500 S SO4 A 1369 O4 SO4 A 1369 4556 1.52 REMARK 500 S SO4 A 1369 O2 SO4 A 1369 4556 1.66 REMARK 500 S SO4 A 1369 O3 SO4 A 1369 4556 1.76 REMARK 500 O1 SO4 A 1369 O3 SO4 A 1369 4556 1.77 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 SER A 92 -105.37 -6.70 REMARK 500 ASP A 151 -151.61 -119.54 REMARK 500 ARG A 204 -3.05 79.61 REMARK 500 ASP A 205 51.54 -149.42 REMARK 500 ASP A 223 75.56 71.05 REMARK 500 SEP A 241 -77.59 99.76 REMARK 500 ASN A 349 42.47 -140.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 358 THR A 359 -134.45 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 1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1365 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1369 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MH4 A 1360 REMARK 900 REMARK 900 RELATED ENTRIES 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: 1OKY RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE 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]AMINO] REMARK 900 PROPYL]-2,2- DIMETHYLPROPANEDIAMIDECOMPLEXED WITH HUMAN PDK1 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: 1OKZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01 REMARK 900 RELATED ID: 1W1D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO INOSITOL (1, 3,4,5)-TETRAKISPHOSPHATE REMARK 900 RELATED ID: 2XCH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1H1W RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN REMARK 900 RELATED ID: 2VKI RELATED DB: PDB REMARK 900 STRUCTURE OF THE PDK1 PH DOMAIN K465E MUTANT REMARK 900 RELATED ID: 1UU3 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531 REMARK 900 RELATED ID: 1W1G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO DIC4- PHOSPHATIDYLINOSITOL (3,4,5)-TRISPHOSPHATE REMARK 900 RELATED ID: 2BIY RELATED DB: PDB REMARK 900 STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN REMARK 900 RELATED ID: 1W1H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN 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: 1UVR RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 DBREF 2XCK A 51 359 UNP O15530 PDPK1_HUMAN 1 309 SEQADV 2XCK THR A 96 UNP O15530 VAL 46 CONFLICT SEQRES 1 A 309 MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY ALA GLY SEQRES 2 A 309 SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG LYS SEQRES 3 A 309 LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU GLY SEQRES 4 A 309 GLU GLY SER PHE SER THR THR VAL LEU ALA ARG GLU LEU SEQRES 5 A 309 ALA THR SER ARG GLU TYR ALA ILE LYS ILE LEU GLU LYS SEQRES 6 A 309 ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR VAL THR SEQRES 7 A 309 ARG GLU ARG ASP VAL MET SER ARG LEU ASP HIS PRO PHE SEQRES 8 A 309 PHE VAL LYS LEU TYR PHE THR PHE GLN ASP ASP GLU LYS SEQRES 9 A 309 LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU LEU SEQRES 10 A 309 LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU THR SEQRES 11 A 309 CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA LEU SEQRES 12 A 309 GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP LEU SEQRES 13 A 309 LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS ILE SEQRES 14 A 309 GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER PRO SEQRES 15 A 309 GLU SER LYS GLN ALA ARG ALA ASN SEP PHE VAL GLY THR SEQRES 16 A 309 ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SER SEQRES 17 A 309 ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS ILE SEQRES 18 A 309 ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG ALA SEQRES 19 A 309 GLY ASN GLU TYR LEU ILE PHE GLN LYS ILE ILE LYS LEU SEQRES 20 A 309 GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA ARG SEQRES 21 A 309 ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR LYS SEQRES 22 A 309 ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO LEU SEQRES 23 A 309 LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU ASN SEQRES 24 A 309 LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 2XCK SEP A 241 SER PHOSPHOSERINE HET SEP A 241 10 HET MH4 A1360 39 HET GOL A1361 6 HET GOL A1362 6 HET GOL A1363 6 HET GOL A1365 6 HET SO4 A1368 5 HET SO4 A1369 5 HET SO4 A1370 5 HETNAM SEP PHOSPHOSERINE HETNAM MH4 1-METHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-N- HETNAM 2 MH4 [(2-METHYLPYRIDIN-4-YL)METHYL]-4,5-DIHYDRO-1H- HETNAM 3 MH4 PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 MH4 C29 H33 N9 O FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 SO4 3(O4 S 2-) FORMUL 10 HOH *139(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 ARG A 136 1 14 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 ASN A 349 GLN A 353 5 5 SHEET 1 AA 5 PHE A 82 GLY A 91 0 SHEET 2 AA 5 SER A 94 GLU A 101 -1 O SER A 94 N GLY A 91 SHEET 3 AA 5 GLU A 107 GLU A 114 -1 O TYR A 108 N ALA A 99 SHEET 4 AA 5 LYS A 154 LEU A 159 -1 O LEU A 155 N LEU A 113 SHEET 5 AA 5 LEU A 145 GLN A 150 -1 N TYR A 146 O GLY A 158 SHEET 1 AB 2 ILE A 201 ILE A 202 0 SHEET 2 AB 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 SHEET 1 AC 2 ILE A 211 LEU A 213 0 SHEET 2 AC 2 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 LINK C ASN A 240 N SEP A 241 1555 1555 1.33 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 SITE 1 AC1 10 ALA A 103 THR A 104 HIS A 139 SER A 191 SITE 2 AC1 10 TRP A 347 GLU A 348 ASN A 349 LEU A 350 SITE 3 AC1 10 HIS A 351 HOH A2057 SITE 1 AC2 7 PHE A 82 LYS A 83 PHE A 84 GLU A 194 SITE 2 AC2 7 GLY A 334 LYS A 337 HOH A2139 SITE 1 AC3 7 ARG A 106 GLU A 107 TYR A 146 SER A 160 SITE 2 AC3 7 TYR A 161 GOL A1365 SO4 A1370 SITE 1 AC4 6 ARG A 106 GLU A 107 HIS A 351 GLN A 352 SITE 2 AC4 6 GOL A1363 SO4 A1370 SITE 1 AC5 5 LYS A 76 ARG A 131 THR A 148 PHE A 149 SITE 2 AC5 5 GLN A 150 SITE 1 AC6 2 LYS A 144 TYR A 146 SITE 1 AC7 4 ARG A 106 HIS A 351 GOL A1363 GOL A1365 SITE 1 AC8 12 LEU A 88 GLY A 91 SER A 94 ALA A 109 SITE 2 AC8 12 LYS A 111 LEU A 159 SER A 160 ALA A 162 SITE 3 AC8 12 LEU A 212 THR A 222 ASP A 223 HOH A2136 CRYST1 123.115 123.115 47.240 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 0.008122 0.004690 0.000000 0.00000 SCALE2 0.000000 0.009379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021169 0.00000