HEADER TRANSFERASE 05-MAR-12 4ALW TITLE BENZOFUROPYRIMIDINONE INHIBITORS OF PIM-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIM-1 KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEIN KINASE DOMAIN, RESIDUES 406-717; COMPND 5 EC: 2.7.1.37; COMPND 6 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TRANSFERASE, PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1 EXPDTA X-RAY DIFFRACTION AUTHOR T.J.STOUT,L.ADAMS REVDAT 2 01-MAY-24 4ALW 1 REMARK REVDAT 1 16-JAN-13 4ALW 0 JRNL AUTH A.L.TSUHAKO,D.S.BROWN,E.S.KOLTUN,N.AAY,A.ARCALAS,V.CHAN, JRNL AUTH 2 H.DU,S.ENGST,M.FRANZINI,A.GALAN,P.HUANG,S.JOHNSTON,B.KANE, JRNL AUTH 3 M.H.KIM,A.D.LAIRD,R.LIN,L.MOCK,I.NGAN,M.PACK,G.STOTT, JRNL AUTH 4 T.J.STOUT,P.YU,C.ZAHARIA,W.ZHANG,P.ZHOU,J.M.NUSS, JRNL AUTH 5 P.C.KEARNEY,W.XU JRNL TITL THE DESIGN, SYNTHESIS, AND BIOLOGICAL EVALUATION OF PIM JRNL TITL 2 KINASE INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 22 3732 2012 JRNL REFN ISSN 0960-894X JRNL PMID 22542012 JRNL DOI 10.1016/J.BMCL.2012.04.025 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 31220 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1670 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) : 2214 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.4740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.009 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2363 ; 0.031 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3211 ; 2.238 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 6.771 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;33.585 ;23.065 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;13.795 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.316 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.191 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1841 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1238 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1614 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 298 ; 0.231 ; 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): 43 ; 0.213 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.278 ; 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): 1427 ; 1.845 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2231 ; 2.715 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1141 ; 4.345 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 976 ; 6.036 ; 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 : BABINET MODEL WITH MASK 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 4ALW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1290051570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 155 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33275 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 37.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3300 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.92 REMARK 200 R MERGE FOR SHELL (I) : 1.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IN-HOUSE PIM1 STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 54.00200 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 27.00100 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 40.50150 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 13.50050 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 67.50250 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 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 -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 GLY A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 LEU A 2 REMARK 465 LEU A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 6 REMARK 465 ASN A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 ALA A 10 REMARK 465 HIS A 11 REMARK 465 LEU A 12 REMARK 465 ARG A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 PRO A 16 REMARK 465 CYS A 17 REMARK 465 ASN A 18 REMARK 465 ASP A 19 REMARK 465 LEU A 20 REMARK 465 HIS A 21 REMARK 465 ALA A 22 REMARK 465 THR A 23 REMARK 465 LYS A 24 REMARK 465 LEU A 25 REMARK 465 ALA A 26 REMARK 465 PRO A 27 REMARK 465 GLY A 28 REMARK 465 LYS A 29 REMARK 465 GLU A 30 REMARK 465 LYS A 31 REMARK 465 GLU A 32 REMARK 465 PRO A 33 REMARK 465 LEU A 307 REMARK 465 SER A 308 REMARK 465 PRO A 309 REMARK 465 GLY A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 LYS A 313 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 O HOH A 2026 O HOH A 2064 1.78 REMARK 500 O HOH A 2025 O HOH A 2064 1.78 REMARK 500 O HOH A 2138 O HOH A 2295 1.97 REMARK 500 O HOH A 2238 O HOH A 2243 2.00 REMARK 500 OG SER A 222 C2 IMD A 1309 2.03 REMARK 500 O HOH A 2194 O HOH A 2196 2.04 REMARK 500 O HOH A 2058 O HOH A 2214 2.10 REMARK 500 O HOH A 2117 O HOH A 2123 2.11 REMARK 500 OD1 ASP A 72 O HOH A 2047 2.14 REMARK 500 O HOH A 2016 O HOH A 2336 2.17 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 O HOH A 2277 O HOH A 2325 3655 1.99 REMARK 500 O HOH A 2078 O HOH A 2289 2544 2.13 REMARK 500 O HOH A 2114 O HOH A 2270 2544 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 52 CB VAL A 52 CG2 -0.127 REMARK 500 PHE A 147 CD1 PHE A 147 CE1 0.126 REMARK 500 TYR A 207 CD1 TYR A 207 CE1 0.091 REMARK 500 GLU A 262 CG GLU A 262 CD 0.120 REMARK 500 GLU A 262 CD GLU A 262 OE1 0.077 REMARK 500 TRP A 269 CG TRP A 269 CD1 0.092 REMARK 500 PHE A 281 CD1 PHE A 281 CE1 0.129 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 57 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 LEU A 118 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 268 NE - CZ - NH1 ANGL. DEV. = -3.7 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 167 46.78 -140.86 REMARK 500 ASP A 186 81.46 71.12 REMARK 500 ASP A 202 32.20 -140.98 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 GLU A 35 SER A 36 146.50 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 IMD A 1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HY7 A 1308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 1309 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XQZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE AT 2.1 A RESOLUTION REMARK 900 RELATED ID: 1XR1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HPIM-1 KINASE IN COMPLEX WITH AMP-PNPAT 2.1 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 1XWS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 KINASE DOMAIN REMARK 900 RELATED ID: 1YHS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO STAUROSPORINE REMARK 900 RELATED ID: 1YI3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM-1 BOUND TO LY294002 REMARK 900 RELATED ID: 1YI4 RELATED DB: PDB REMARK 900 STRUCTURE OF PIM-1 BOUND TO ADENOSINE REMARK 900 RELATED ID: 1YWV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF PROTO-ONCOGENE KINASE PIM1: A TARGETOF REMARK 900 ABERRANT SOMATIC HYPERMUTATIONS IN DIFFUSE LARGE CELLLYMPHOMA REMARK 900 RELATED ID: 1YXS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 WITH P123M MUTATION REMARK 900 RELATED ID: 1YXT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH AMPPNP REMARK 900 RELATED ID: 1YXU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH AMP REMARK 900 RELATED ID: 1YXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH 3,4 -DIHYDROXY-1- REMARK 900 METHYLQUINOLIN-2(1H)-ONE REMARK 900 RELATED ID: 1YXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF KINASE PIM1 IN COMPLEX WITH (3E )-3-[(4- REMARK 900 HYDROXYPHENYL)IMINO]-1H-INDOL-2(3H)-ONE REMARK 900 RELATED ID: 2BIK RELATED DB: PDB REMARK 900 HUMAN PIM1 PHOSPHORYLATED ON SER261 REMARK 900 RELATED ID: 2BIL RELATED DB: PDB REMARK 900 THE HUMAN PROTEIN KINASE PIM1 IN COMPLEX WITH ITS CONSENSUS PEPTIDE REMARK 900 PIMTIDE REMARK 900 RELATED ID: 2BZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU1 REMARK 900 RELATED ID: 2BZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU2 REMARK 900 RELATED ID: 2BZJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM REMARK 900 ORGANOMETALLIC LIGAND RU3 REMARK 900 RELATED ID: 2BZK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND REMARK 900 PIMTIDE REMARK 900 RELATED ID: 2C3I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH IMIDAZOPYRIDAZIN I REMARK 900 RELATED ID: 2J2I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAB PIM1 IN COMPLEX WITH LY333531 REMARK 900 RELATED ID: 2XIX RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-1 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2XIY RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-2 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2XIZ RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-3 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2XJ0 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH FRAGMENT-4 FROM REMARK 900 CRYSTALLOGRAPHIC FRAGMENT SCREEN REMARK 900 RELATED ID: 2XJ1 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH SMALL MOLECULE INIBITOR REMARK 900 RELATED ID: 2XJ2 RELATED DB: PDB REMARK 900 PROTEIN KINASE PIM-1 IN COMPLEX WITH SMALL MOLECULE INHIBITOR REMARK 900 RELATED ID: 4A7C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PIM1 KINASE WITH ETP46546 DBREF 4ALW A 2 313 UNP P11309 PIM1_HUMAN 2 213 SEQADV 4ALW MET A -14 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -13 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -12 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -11 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -10 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -9 UNP P11309 EXPRESSION TAG SEQADV 4ALW HIS A -8 UNP P11309 EXPRESSION TAG SEQADV 4ALW GLY A -7 UNP P11309 EXPRESSION TAG SEQADV 4ALW GLU A -6 UNP P11309 EXPRESSION TAG SEQADV 4ALW ASN A -5 UNP P11309 EXPRESSION TAG SEQADV 4ALW LEU A -4 UNP P11309 EXPRESSION TAG SEQADV 4ALW TYR A -3 UNP P11309 EXPRESSION TAG SEQADV 4ALW PHE A -2 UNP P11309 EXPRESSION TAG SEQADV 4ALW GLN A -1 UNP P11309 EXPRESSION TAG SEQADV 4ALW GLY A 0 UNP P11309 EXPRESSION TAG SEQADV 4ALW SER A 1 UNP P11309 EXPRESSION TAG SEQRES 1 A 328 MET HIS HIS HIS HIS HIS HIS GLY GLU ASN LEU TYR PHE SEQRES 2 A 328 GLN GLY SER LEU LEU SER LYS ILE ASN SER LEU ALA HIS SEQRES 3 A 328 LEU ARG ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS SEQRES 4 A 328 LEU ALA PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN SEQRES 5 A 328 TYR GLN VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SEQRES 6 A 328 SER VAL TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO SEQRES 7 A 328 VAL ALA ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP SEQRES 8 A 328 TRP GLY GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU SEQRES 9 A 328 VAL VAL LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY SEQRES 10 A 328 VAL ILE ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER SEQRES 11 A 328 PHE VAL LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP SEQRES 12 A 328 LEU PHE ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU SEQRES 13 A 328 GLU LEU ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA SEQRES 14 A 328 VAL ARG HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP SEQRES 15 A 328 ILE LYS ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY SEQRES 16 A 328 GLU LEU LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU SEQRES 17 A 328 LYS ASP THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL SEQRES 18 A 328 TYR SER PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS SEQRES 19 A 328 GLY ARG SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU SEQRES 20 A 328 TYR ASP MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP SEQRES 21 A 328 GLU GLU ILE ILE ARG GLY GLN VAL PHE PHE ARG GLN ARG SEQRES 22 A 328 VAL SER SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU SEQRES 23 A 328 ALA LEU ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE SEQRES 24 A 328 GLN ASN HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN SEQRES 25 A 328 GLU THR ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY SEQRES 26 A 328 PRO SER LYS HET IMD A1307 5 HET HY7 A1308 23 HET IMD A1309 5 HETNAM IMD IMIDAZOLE HETNAM HY7 8-BROMANYL-2-[(4-METHYLPIPERAZIN-1-YL)METHYL]-3H- HETNAM 2 HY7 [1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE FORMUL 2 IMD 2(C3 H5 N2 1+) FORMUL 3 HY7 C16 H17 BR N4 O2 FORMUL 5 HOH *337(H2 O) HELIX 1 1 ASP A 72 ILE A 74 5 3 HELIX 2 2 MET A 88 SER A 97 1 10 HELIX 3 3 LEU A 129 GLY A 137 1 9 HELIX 4 4 GLN A 140 CYS A 161 1 22 HELIX 5 5 LYS A 169 GLU A 171 5 3 HELIX 6 6 ASP A 186 GLY A 190 5 5 HELIX 7 7 THR A 204 SER A 208 5 5 HELIX 8 8 PRO A 209 HIS A 216 1 8 HELIX 9 9 HIS A 219 GLY A 238 1 20 HELIX 10 10 HIS A 244 GLY A 251 1 8 HELIX 11 11 SER A 260 LEU A 271 1 12 HELIX 12 12 ARG A 274 ARG A 278 5 5 HELIX 13 13 THR A 280 ASN A 286 1 7 HELIX 14 14 HIS A 287 GLN A 291 5 5 HELIX 15 15 LEU A 295 LEU A 304 1 10 SHEET 1 AA 5 TYR A 38 GLY A 47 0 SHEET 2 AA 5 GLY A 50 ARG A 57 -1 O GLY A 50 N GLY A 47 SHEET 3 AA 5 LEU A 62 GLU A 70 -1 O LEU A 62 N ARG A 57 SHEET 4 AA 5 SER A 115 GLU A 121 -1 O PHE A 116 N VAL A 69 SHEET 5 AA 5 LEU A 106 GLU A 111 -1 N LEU A 107 O ILE A 119 SHEET 1 AB 2 TRP A 77 GLU A 79 0 SHEET 2 AB 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 AC 3 VAL A 126 ASP A 128 0 SHEET 2 AC 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 AC 3 GLU A 181 LEU A 184 -1 O GLU A 181 N ASP A 176 SHEET 1 AD 2 VAL A 163 LEU A 164 0 SHEET 2 AD 2 ALA A 191 LEU A 192 -1 O ALA A 191 N LEU A 164 CISPEP 1 GLU A 124 PRO A 125 0 0.04 SITE 1 AC1 7 PHE A 130 ILE A 133 THR A 134 ASP A 170 SITE 2 AC1 7 ASP A 234 GLY A 238 ASP A 239 SITE 1 AC2 13 PHE A 49 VAL A 52 ALA A 65 LYS A 67 SITE 2 AC2 13 LEU A 120 GLU A 121 ASN A 172 LEU A 174 SITE 3 AC2 13 ILE A 185 ASP A 186 HOH A2213 HOH A2336 SITE 4 AC2 13 HOH A2337 SITE 1 AC3 5 HIS A 219 ARG A 221 SER A 222 HOH A2249 SITE 2 AC3 5 HOH A2302 CRYST1 97.449 97.449 81.003 90.00 90.00 120.00 P 65 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 0.010262 0.005925 0.000000 0.00000 SCALE2 0.000000 0.011849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012345 0.00000