HEADER TRANSFERASE/TRANSFERASE INHIBITOR 22-SEP-16 5TEL 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 33-306; 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, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.MECHIN,R.WANG,J.D.BATCHELOR REVDAT 2 04-OCT-23 5TEL 1 REMARK REVDAT 1 11-OCT-17 5TEL 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. 2.21 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 20718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.610 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 31.1036 - 5.3289 1.00 1440 153 0.1690 0.1780 REMARK 3 2 5.3289 - 4.2331 0.99 1406 145 0.1541 0.1708 REMARK 3 3 4.2331 - 3.6990 0.99 1411 147 0.1663 0.1961 REMARK 3 4 3.6990 - 3.3612 1.00 1402 151 0.1708 0.2014 REMARK 3 5 3.3612 - 3.1206 0.99 1395 149 0.1848 0.2231 REMARK 3 6 3.1206 - 2.9367 0.98 1358 148 0.1943 0.2129 REMARK 3 7 2.9367 - 2.7897 0.97 1355 140 0.1893 0.2348 REMARK 3 8 2.7897 - 2.6684 0.96 1358 146 0.2066 0.2700 REMARK 3 9 2.6684 - 2.5657 0.94 1322 143 0.1991 0.2396 REMARK 3 10 2.5657 - 2.4772 0.93 1303 145 0.1984 0.2252 REMARK 3 11 2.4772 - 2.3998 0.92 1287 141 0.2009 0.2414 REMARK 3 12 2.3998 - 2.3312 0.92 1285 134 0.2040 0.2455 REMARK 3 13 2.3312 - 2.2698 0.90 1262 124 0.2080 0.2543 REMARK 3 14 2.2698 - 2.2145 0.81 1144 124 0.2251 0.2514 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.030 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 : 0.003 2339 REMARK 3 ANGLE : 0.698 3177 REMARK 3 CHIRALITY : 0.045 333 REMARK 3 PLANARITY : 0.004 411 REMARK 3 DIHEDRAL : 12.734 1374 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 5TEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000224103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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: PHASER 2.6.0 REMARK 200 STARTING MODEL: 1YXT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: IMIDAZOLE 0,1M - NAACETATE 0,7M - REMARK 280 PH6,5, 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 53.85867 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 26.92933 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 40.39400 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 13.46467 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 67.32333 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 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 NH1 ARG A 122 OE1 GLU A 124 2.04 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 41.93 -145.99 REMARK 500 ASP A 186 78.29 61.02 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7AJ A 402 DBREF 5TEL A 33 306 UNP P11309 PIM1_HUMAN 33 306 SEQRES 1 A 274 PRO LEU GLU SER GLN TYR GLN VAL GLY PRO LEU LEU GLY SEQRES 2 A 274 SER GLY GLY PHE GLY SER VAL TYR SER GLY ILE ARG VAL SEQRES 3 A 274 SER ASP ASN LEU PRO VAL ALA ILE LYS HIS VAL GLU LYS SEQRES 4 A 274 ASP ARG ILE SER ASP TRP GLY GLU LEU PRO ASN GLY THR SEQRES 5 A 274 ARG VAL PRO MET GLU VAL VAL LEU LEU LYS LYS VAL SER SEQRES 6 A 274 SER GLY PHE SER GLY VAL ILE ARG LEU LEU ASP TRP PHE SEQRES 7 A 274 GLU ARG PRO ASP SER PHE VAL LEU ILE LEU GLU ARG PRO SEQRES 8 A 274 GLU PRO VAL GLN ASP LEU PHE ASP PHE ILE THR GLU ARG SEQRES 9 A 274 GLY ALA LEU GLN GLU GLU LEU ALA ARG SER PHE PHE TRP SEQRES 10 A 274 GLN VAL LEU GLU ALA VAL ARG HIS CYS HIS ASN CYS GLY SEQRES 11 A 274 VAL LEU HIS ARG ASP ILE LYS ASP GLU ASN ILE LEU ILE SEQRES 12 A 274 ASP LEU ASN ARG GLY GLU LEU LYS LEU ILE ASP PHE GLY SEQRES 13 A 274 SER GLY ALA LEU LEU LYS ASP THR VAL TYR THR ASP PHE SEQRES 14 A 274 ASP GLY THR ARG VAL TYR SER PRO PRO GLU TRP ILE ARG SEQRES 15 A 274 TYR HIS ARG TYR HIS GLY ARG SER ALA ALA VAL TRP SER SEQRES 16 A 274 LEU GLY ILE LEU LEU TYR ASP MET VAL CYS GLY ASP ILE SEQRES 17 A 274 PRO PHE GLU HIS ASP GLU GLU ILE ILE ARG GLY GLN VAL SEQRES 18 A 274 PHE PHE ARG GLN ARG VAL SER SER GLU CYS GLN HIS LEU SEQRES 19 A 274 ILE ARG TRP CYS LEU ALA LEU ARG PRO SER ASP ARG PRO SEQRES 20 A 274 THR PHE GLU GLU ILE GLN ASN HIS PRO TRP MET GLN ASP SEQRES 21 A 274 VAL LEU LEU PRO GLN GLU THR ALA GLU ILE HIS LEU HIS SEQRES 22 A 274 SER HET IMD A 401 5 HET 7AJ A 402 32 HETNAM IMD IMIDAZOLE HETNAM 7AJ 4-CHLORO-2-{5,6-DIMETHOXY-1-[2-(4-METHYLPIPERAZIN-1- HETNAM 2 7AJ YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLO[2,3-B]PYRIDINE FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 7AJ C24 H28 CL N5 O2 FORMUL 4 HOH *159(H2 O) HELIX 1 AA1 ASP A 72 ILE A 74 5 3 HELIX 2 AA2 MET A 88 SER A 97 1 10 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 ASN A 286 1 7 HELIX 13 AB4 HIS A 287 GLN A 291 5 5 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 LEU A 62 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 PHE A 110 O VAL A 117 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 GLU A 181 N ASP A 176 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 LINK NH1 ARG A 221 CB SER A 222 1555 1555 1.48 CISPEP 1 GLU A 124 PRO A 125 0 -1.40 SITE 1 AC1 5 PHE A 130 THR A 134 ASP A 170 ASP A 234 SITE 2 AC1 5 GLY A 238 SITE 1 AC2 12 LEU A 44 ALA A 65 VAL A 126 ASP A 128 SITE 2 AC2 12 ASP A 131 GLU A 171 LEU A 174 ILE A 185 SITE 3 AC2 12 HOH A 504 HOH A 542 HOH A 552 HOH A 563 CRYST1 97.474 97.474 80.788 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 0.010259 0.005923 0.000000 0.00000 SCALE2 0.000000 0.011846 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012378 0.00000