HEADER TRANSFERASE/TRANSFERASE INHIBITOR 07-MAR-11 3R04 TITLE THE DISCOVERY OF NOVEL BENZOFURAN-2-CARBOXYLIC ACIDS AS POTENT PIM-1 TITLE 2 INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.11.1; COMPND 5 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: PIM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINAE, PIM1, INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIANG,B.HIRTH,G.ASMUSSEN,H.-P.BIEMANN,A.GOOD,M.FITZGERALD, AUTHOR 2 T.GLADYSHEVA,K.JANCSICS,J.LIU,M.METZ,A.PAPOULIS,R.SKERLJ,D.J.STEPP, AUTHOR 3 R.R.WEI REVDAT 2 21-FEB-24 3R04 1 REMARK SEQADV REVDAT 1 11-MAY-11 3R04 0 JRNL AUTH Y.XIANG,B.HIRTH,G.ASMUSSEN,H.P.BIEMANN,K.A.BISHOP,A.GOOD, JRNL AUTH 2 M.FITZGERALD,T.GLADYSHEVA,A.JAIN,K.JANCSICS,J.LIU,M.METZ, JRNL AUTH 3 A.PAPOULIS,R.SKERLJ,J.D.STEPP,R.R.WEI JRNL TITL THE DISCOVERY OF NOVEL BENZOFURAN-2-CARBOXYLIC ACIDS AS JRNL TITL 2 POTENT PIM-1 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 21 3050 2011 JRNL REFN ISSN 0960-894X JRNL PMID 21507633 JRNL DOI 10.1016/J.BMCL.2011.03.030 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 45727 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2441 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3114 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2209 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.86000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -1.28000 REMARK 3 B12 (A**2) : 0.43000 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): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.651 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 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): 2315 ; 0.033 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3148 ; 2.341 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.057 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;32.678 ;23.193 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;14.180 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.514 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 333 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1810 ; 0.014 ; 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): 1360 ; 1.511 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2209 ; 2.610 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 955 ; 4.070 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 939 ; 6.345 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 35 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 31.2122 -27.2004 -0.6667 REMARK 3 T TENSOR REMARK 3 T11: 0.0335 T22: 0.0481 REMARK 3 T33: 0.0086 T12: -0.0128 REMARK 3 T13: 0.0104 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.9312 L22: 0.5551 REMARK 3 L33: 1.4744 L12: 0.0493 REMARK 3 L13: 0.2787 L23: -0.0622 REMARK 3 S TENSOR REMARK 3 S11: -0.0427 S12: -0.0179 S13: -0.0222 REMARK 3 S21: 0.0270 S22: 0.0376 S23: 0.0389 REMARK 3 S31: -0.0030 S32: -0.2071 S33: 0.0051 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 3R04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.4 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45727 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 84.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, 1-1.4 M SODIUM ACETATE REMARK 280 ANHYDROUS, PH 6.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 53.75267 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 26.87633 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 40.31450 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 13.43817 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 67.19083 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 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 34 REMARK 465 SER A 306 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 465 ALA A 314 REMARK 465 ALA A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 REMARK 465 HIS A 323 REMARK 465 HIS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 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 337 O HOH A 502 1.29 REMARK 500 O HOH A 467 O HOH A 517 1.82 REMARK 500 O HOH A 370 O HOH A 529 1.87 REMARK 500 O HOH A 7 O HOH A 453 1.87 REMARK 500 O HOH A 353 O HOH A 501 1.88 REMARK 500 O HOH A 26 O HOH A 475 1.91 REMARK 500 O HOH A 13 O HOH A 513 1.95 REMARK 500 O HOH A 487 O HOH A 501 2.04 REMARK 500 O HOH A 13 O HOH A 517 2.04 REMARK 500 O HOH A 423 O HOH A 494 2.04 REMARK 500 O HOH A 338 O HOH A 436 2.10 REMARK 500 O HOH A 13 O HOH A 503 2.11 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 376 O HOH A 396 2544 2.07 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 PHE A 100 CE1 PHE A 100 CZ 0.168 REMARK 500 ASN A 160 CB ASN A 160 CG -0.148 REMARK 500 MET A 235 SD MET A 235 CE -0.446 REMARK 500 GLU A 246 CG GLU A 246 CD 0.125 REMARK 500 ARG A 258 CZ ARG A 258 NH1 0.173 REMARK 500 ARG A 258 CZ ARG A 258 NH2 0.115 REMARK 500 SER A 260 CA SER A 260 CB 0.090 REMARK 500 TRP A 269 CE3 TRP A 269 CZ3 0.106 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. = 3.4 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 128 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 PHE A 147 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 170 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 LEU A 174 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 239 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 258 NH1 - CZ - NH2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = -6.2 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 PRO A 81 66.17 -56.16 REMARK 500 ASN A 82 -2.95 177.95 REMARK 500 SER A 98 173.97 168.21 REMARK 500 GLU A 124 114.54 -163.27 REMARK 500 ASP A 167 41.60 -146.23 REMARK 500 ASP A 186 74.31 65.61 REMARK 500 ASP A 202 31.05 -140.54 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 UNQ A 555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 4496 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 4497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 4498 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R00 RELATED DB: PDB REMARK 900 RELATED ID: 3R01 RELATED DB: PDB REMARK 900 RELATED ID: 3R02 RELATED DB: PDB DBREF 3R04 A 29 313 UNP P11309 PIM1_HUMAN 120 404 SEQADV 3R04 MET A 28 UNP P11309 INITIATING METHIONINE SEQADV 3R04 ALA A 314 UNP P11309 EXPRESSION TAG SEQADV 3R04 ALA A 315 UNP P11309 EXPRESSION TAG SEQADV 3R04 ALA A 316 UNP P11309 EXPRESSION TAG SEQADV 3R04 LEU A 317 UNP P11309 EXPRESSION TAG SEQADV 3R04 GLU A 318 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 319 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 320 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 321 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 322 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 323 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 324 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 325 UNP P11309 EXPRESSION TAG SEQADV 3R04 HIS A 326 UNP P11309 EXPRESSION TAG SEQRES 1 A 299 MET LYS GLU LYS GLU PRO LEU GLU SER GLN TYR GLN VAL SEQRES 2 A 299 GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER VAL TYR SEQRES 3 A 299 SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL ALA ILE SEQRES 4 A 299 LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP GLY GLU SEQRES 5 A 299 LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL VAL LEU SEQRES 6 A 299 LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL ILE ARG SEQRES 7 A 299 LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE VAL LEU SEQRES 8 A 299 ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU PHE ASP SEQRES 9 A 299 PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU LEU ALA SEQRES 10 A 299 ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL ARG HIS SEQRES 11 A 299 CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE LYS ASP SEQRES 12 A 299 GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU LEU LYS SEQRES 13 A 299 LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS ASP THR SEQRES 14 A 299 VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR SER PRO SEQRES 15 A 299 PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY ARG SER SEQRES 16 A 299 ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR ASP MET SEQRES 17 A 299 VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU GLU ILE SEQRES 18 A 299 ILE ARG GLY GLN VAL PHE PHE ARG GLN ARG VAL SER SER SEQRES 19 A 299 GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA LEU ARG SEQRES 20 A 299 PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN ASN HIS SEQRES 21 A 299 PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU THR ALA SEQRES 22 A 299 GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO SER LYS SEQRES 23 A 299 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HIS HIS HET UNQ A 555 26 HET IMD A4496 5 HET IMD A4497 5 HET IMD A4498 5 HETNAM UNQ 5-{6-[(TRANS-4-AMINOCYCLOHEXYL)AMINO]PYRAZIN-2-YL}-1- HETNAM 2 UNQ BENZOFURAN-2-CARBOXYLIC ACID HETNAM IMD IMIDAZOLE FORMUL 2 UNQ C19 H20 N4 O3 FORMUL 3 IMD 3(C3 H5 N2 1+) FORMUL 6 HOH *231(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 THR A 204 SER A 208 5 5 HELIX 7 7 PRO A 209 HIS A 216 1 8 HELIX 8 8 HIS A 219 GLY A 238 1 20 HELIX 9 9 HIS A 244 GLY A 251 1 8 HELIX 10 10 SER A 260 LEU A 271 1 12 HELIX 11 11 ARG A 274 ARG A 278 5 5 HELIX 12 12 THR A 280 ASN A 286 1 7 HELIX 13 13 HIS A 287 GLN A 291 5 5 HELIX 14 14 LEU A 295 LEU A 304 1 10 SHEET 1 A 5 TYR A 38 GLY A 47 0 SHEET 2 A 5 GLY A 50 ARG A 57 -1 O SER A 54 N GLY A 41 SHEET 3 A 5 LEU A 62 GLU A 70 -1 O HIS A 68 N SER A 51 SHEET 4 A 5 SER A 115 GLU A 121 -1 O LEU A 118 N LYS A 67 SHEET 5 A 5 LEU A 106 ARG A 112 -1 N LEU A 107 O ILE A 119 SHEET 1 B 2 TRP A 77 GLU A 79 0 SHEET 2 B 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 C 3 VAL A 126 ASP A 128 0 SHEET 2 C 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 C 3 GLU A 181 LEU A 184 -1 O GLU A 181 N ASP A 176 SHEET 1 D 2 VAL A 163 LEU A 164 0 SHEET 2 D 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 18.33 CISPEP 2 GLU A 124 PRO A 125 0 -14.46 SITE 1 AC1 16 HOH A 18 LEU A 44 ALA A 65 LYS A 67 SITE 2 AC1 16 LEU A 120 GLU A 121 ARG A 122 VAL A 126 SITE 3 AC1 16 ASP A 128 LEU A 174 ASP A 186 HOH A 327 SITE 4 AC1 16 HOH A 332 HOH A 415 HOH A 439 HOH A 504 SITE 1 AC2 4 VAL A 206 ILE A 240 GLU A 243 HOH A 379 SITE 1 AC3 6 PHE A 130 THR A 134 ASP A 170 ASP A 234 SITE 2 AC3 6 GLY A 238 ASP A 239 SITE 1 AC4 2 PHE A 130 GLU A 171 CRYST1 97.941 97.941 80.629 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 0.010210 0.005895 0.000000 0.00000 SCALE2 0.000000 0.011790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012402 0.00000