HEADER TRANSFERASE/TRANSFERASE INHIBITOR 17-OCT-16 5TOE TITLE PIM-1 KINASE IN COMPLEX WITH A 7-AZAINDOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PIM-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 34-306; COMPND 5 EC: 2.7.11.1; 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 GENE: PIM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, INHIBITOR, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.MCLEAN,I.MECHIN,Y.ZHANG,R.WANG,J.D.BATCHELOR REVDAT 2 06-MAR-24 5TOE 1 REMARK REVDAT 1 11-OCT-17 5TOE 0 JRNL AUTH C.BARBERIS,N.MOORCROFT,C.ARENDT,M.LEVIT,S.MORENO-MAZZA, JRNL AUTH 2 J.BATCHELOR,I.MECHIN,T.MAJID JRNL TITL DISCOVERY OF N-SUBSTITUTED 7-AZAINDOLES AS PIM1 KINASE JRNL TITL 2 INHIBITORS - PART I. JRNL REF BIOORG. MED. CHEM. LETT. V. 27 4730 2017 JRNL REFN ESSN 1464-3405 JRNL PMID 28947155 JRNL DOI 10.1016/J.BMCL.2017.08.069 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 18965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1892 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.1158 - 5.5420 1.00 1280 145 0.1719 0.1906 REMARK 3 2 5.5420 - 4.4004 1.00 1250 146 0.1556 0.1857 REMARK 3 3 4.4004 - 3.8446 1.00 1250 134 0.1537 0.2158 REMARK 3 4 3.8446 - 3.4932 1.00 1258 140 0.1636 0.2124 REMARK 3 5 3.4932 - 3.2430 1.00 1232 136 0.1874 0.2416 REMARK 3 6 3.2430 - 3.0518 1.00 1262 146 0.1961 0.2319 REMARK 3 7 3.0518 - 2.8990 1.00 1250 134 0.1958 0.2420 REMARK 3 8 2.8990 - 2.7729 1.00 1252 136 0.2008 0.2520 REMARK 3 9 2.7729 - 2.6661 1.00 1225 132 0.2341 0.3089 REMARK 3 10 2.6661 - 2.5741 1.00 1248 136 0.2403 0.2666 REMARK 3 11 2.5741 - 2.4937 0.99 1214 131 0.2537 0.3203 REMARK 3 12 2.4937 - 2.4224 0.95 1188 135 0.2732 0.3191 REMARK 3 13 2.4224 - 2.3586 0.90 1125 122 0.3012 0.3151 REMARK 3 14 2.3586 - 2.3011 0.85 1039 119 0.2993 0.3465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 2304 REMARK 3 ANGLE : 1.311 3127 REMARK 3 CHIRALITY : 0.056 331 REMARK 3 PLANARITY : 0.006 406 REMARK 3 DIHEDRAL : 14.802 1354 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TOE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18965 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.301 REMARK 200 RESOLUTION RANGE LOW (A) : 42.109 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.7600 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, 1M NAACETATE, 20% REMARK 280 GLYCEROL PH 6.5, VAPOR DIFFUSION, TEMPERATURE 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 54.05400 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 27.02700 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 40.54050 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 13.51350 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 67.56750 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 GLY A 83 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 CD2 PHE A 100 OE1 GLN A 252 3665 1.65 REMARK 500 CG PHE A 100 OE1 GLN A 252 3665 1.86 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 60 13.61 -147.84 REMARK 500 SER A 101 -168.65 -169.60 REMARK 500 ASP A 167 44.97 -150.21 REMARK 500 ASP A 186 79.11 66.65 REMARK 500 HIS A 305 33.83 71.29 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 7GK A 401 DBREF 5TOE A 34 306 UNP P11309 PIM1_HUMAN 34 306 SEQRES 1 A 273 LEU GLU SER GLN TYR GLN VAL GLY PRO LEU LEU GLY SER SEQRES 2 A 273 GLY GLY PHE GLY SER VAL TYR SER GLY ILE ARG VAL SER SEQRES 3 A 273 ASP ASN LEU PRO VAL ALA ILE LYS HIS VAL GLU LYS ASP SEQRES 4 A 273 ARG ILE SER ASP TRP GLY GLU LEU PRO ASN GLY THR ARG SEQRES 5 A 273 VAL PRO MET GLU VAL VAL LEU LEU LYS LYS VAL SER SER SEQRES 6 A 273 GLY PHE SER GLY VAL ILE ARG LEU LEU ASP TRP PHE GLU SEQRES 7 A 273 ARG PRO ASP SER PHE VAL LEU ILE LEU GLU ARG PRO GLU SEQRES 8 A 273 PRO VAL GLN ASP LEU PHE ASP PHE ILE THR GLU ARG GLY SEQRES 9 A 273 ALA LEU GLN GLU GLU LEU ALA ARG SER PHE PHE TRP GLN SEQRES 10 A 273 VAL LEU GLU ALA VAL ARG HIS CYS HIS ASN CYS GLY VAL SEQRES 11 A 273 LEU HIS ARG ASP ILE LYS ASP GLU ASN ILE LEU ILE ASP SEQRES 12 A 273 LEU ASN ARG GLY GLU LEU LYS LEU ILE ASP PHE GLY SER SEQRES 13 A 273 GLY ALA LEU LEU LYS ASP THR VAL TYR THR ASP PHE ASP SEQRES 14 A 273 GLY THR ARG VAL TYR SER PRO PRO GLU TRP ILE ARG TYR SEQRES 15 A 273 HIS ARG TYR HIS GLY ARG SER ALA ALA VAL TRP SER LEU SEQRES 16 A 273 GLY ILE LEU LEU TYR ASP MET VAL CYS GLY ASP ILE PRO SEQRES 17 A 273 PHE GLU HIS ASP GLU GLU ILE ILE ARG GLY GLN VAL PHE SEQRES 18 A 273 PHE ARG GLN ARG VAL SER SER GLU CYS GLN HIS LEU ILE SEQRES 19 A 273 ARG TRP CYS LEU ALA LEU ARG PRO SER ASP ARG PRO THR SEQRES 20 A 273 PHE GLU GLU ILE GLN ASN HIS PRO TRP MET GLN ASP VAL SEQRES 21 A 273 LEU LEU PRO GLN GLU THR ALA GLU ILE HIS LEU HIS SER HET 7GK A 401 23 HETNAM 7GK 2-[4-(PIPERAZIN-1-YL)PHENYL]-1H-PYRROLO[2,3-B]PYRIDINE- HETNAM 2 7GK 4-CARBONITRILE FORMUL 2 7GK C18 H17 N5 FORMUL 3 HOH *131(H2 O) HELIX 1 AA1 ASP A 72 ILE A 74 5 3 HELIX 2 AA2 MET A 88 SER A 98 1 11 HELIX 3 AA3 LEU A 129 GLY A 137 1 9 HELIX 4 AA4 GLN A 140 CYS A 161 1 22 HELIX 5 AA5 LYS A 169 GLU A 171 5 3 HELIX 6 AA6 THR A 204 SER A 208 5 5 HELIX 7 AA7 PRO A 209 HIS A 216 1 8 HELIX 8 AA8 HIS A 219 GLY A 238 1 20 HELIX 9 AA9 HIS A 244 GLY A 251 1 8 HELIX 10 AB1 SER A 260 LEU A 271 1 12 HELIX 11 AB2 ARG A 274 ARG A 278 5 5 HELIX 12 AB3 THR A 280 HIS A 287 1 8 HELIX 13 AB4 PRO A 288 GLN A 291 5 4 HELIX 14 AB5 LEU A 295 LEU A 304 1 10 SHEET 1 AA1 5 TYR A 38 GLY A 47 0 SHEET 2 AA1 5 GLY A 50 ARG A 57 -1 O SER A 54 N GLY A 41 SHEET 3 AA1 5 PRO A 63 GLU A 70 -1 O ILE A 66 N TYR A 53 SHEET 4 AA1 5 SER A 115 GLU A 121 -1 O LEU A 120 N ALA A 65 SHEET 5 AA1 5 LEU A 106 GLU A 111 -1 N ASP A 108 O ILE A 119 SHEET 1 AA2 2 TRP A 77 GLU A 79 0 SHEET 2 AA2 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78 SHEET 1 AA3 3 VAL A 126 ASP A 128 0 SHEET 2 AA3 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127 SHEET 3 AA3 3 GLU A 181 LEU A 184 -1 O LYS A 183 N LEU A 174 SHEET 1 AA4 2 VAL A 163 LEU A 164 0 SHEET 2 AA4 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 -1.81 SITE 1 AC1 9 LEU A 44 ALA A 65 GLU A 121 ARG A 122 SITE 2 AC1 9 ASP A 131 LEU A 174 ILE A 185 HOH A 545 SITE 3 AC1 9 HOH A 566 CRYST1 97.246 97.246 81.081 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 0.010283 0.005937 0.000000 0.00000 SCALE2 0.000000 0.011874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012333 0.00000