HEADER TRANSFERASE 25-MAY-22 7ZYK TITLE COMPOUND 9 BOUND TO CK2ALPHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASEIN KINASE II SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CK II ALPHA; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CSNK2A1, CK2A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FRAGMENT BASED DRUG DISCOVERY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.BREAR,M.HYVONEN REVDAT 2 31-JAN-24 7ZYK 1 REMARK REVDAT 1 07-DEC-22 7ZYK 0 JRNL AUTH P.BREAR,C.DE FUSCO,E.L.ATKINSON,J.IEGRE,N.J.FRANCIS-NEWTON, JRNL AUTH 2 A.R.VENKITARAMAN,M.HYVONEN,D.R.SPRING JRNL TITL A FRAGMENT-BASED APPROACH LEADING TO THE DISCOVERY OF JRNL TITL 2 INHIBITORS OF CK2 ALPHA WITH A NOVEL MECHANISM OF ACTION. JRNL REF RSC MED CHEM V. 13 1420 2022 JRNL REFN ESSN 2632-8682 JRNL PMID 36426237 JRNL DOI 10.1039/D2MD00161F REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC V1.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 64749 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 3265 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28140 REMARK 3 B22 (A**2) : 1.42350 REMARK 3 B33 (A**2) : -1.14210 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.61980 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979490 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.305 REMARK 200 RESOLUTION RANGE LOW (A) : 54.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.1 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.63100 REMARK 200 R SYM FOR SHELL (I) : 0.63100 REMARK 200 FOR SHELL : 2.600 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: 5MOH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 112.5MM MES PH 6.5, 35% GLYCEROL REMARK 280 ETHOXYLATE, 180 MM AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.92100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 SER A 2 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 156 43.05 -151.39 REMARK 500 ASP A 175 73.49 61.79 REMARK 500 ALA A 193 165.94 64.18 REMARK 500 ALA A 193 166.22 64.18 REMARK 500 MET A 208 54.82 -93.55 REMARK 500 ASP A 210 -159.44 -153.53 REMARK 500 HIS A 234 70.81 -101.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 18 10.10 REMARK 500 ALA A 193 12.13 REMARK 500 ALA A 193 11.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ZYK A 2 329 UNP P68400 CSK21_HUMAN 2 329 SEQADV 7ZYK SER A 21 UNP P68400 ARG 21 ENGINEERED MUTATION SEQADV 7ZYK ALA A 74 UNP P68400 LYS 74 ENGINEERED MUTATION SEQADV 7ZYK ALA A 75 UNP P68400 LYS 75 ENGINEERED MUTATION SEQADV 7ZYK ALA A 76 UNP P68400 LYS 76 ENGINEERED MUTATION SEQRES 1 A 328 SER GLY PRO VAL PRO SER ARG ALA ARG VAL TYR THR ASP SEQRES 2 A 328 VAL ASN THR HIS ARG PRO SER GLU TYR TRP ASP TYR GLU SEQRES 3 A 328 SER HIS VAL VAL GLU TRP GLY ASN GLN ASP ASP TYR GLN SEQRES 4 A 328 LEU VAL ARG LYS LEU GLY ARG GLY LYS TYR SER GLU VAL SEQRES 5 A 328 PHE GLU ALA ILE ASN ILE THR ASN ASN GLU LYS VAL VAL SEQRES 6 A 328 VAL LYS ILE LEU LYS PRO VAL ALA ALA ALA LYS ILE LYS SEQRES 7 A 328 ARG GLU ILE LYS ILE LEU GLU ASN LEU ARG GLY GLY PRO SEQRES 8 A 328 ASN ILE ILE THR LEU ALA ASP ILE VAL LYS ASP PRO VAL SEQRES 9 A 328 SER ARG THR PRO ALA LEU VAL PHE GLU HIS VAL ASN ASN SEQRES 10 A 328 THR ASP PHE LYS GLN LEU TYR GLN THR LEU THR ASP TYR SEQRES 11 A 328 ASP ILE ARG PHE TYR MET TYR GLU ILE LEU LYS ALA LEU SEQRES 12 A 328 ASP TYR CYS HIS SER MET GLY ILE MET HIS ARG ASP VAL SEQRES 13 A 328 LYS PRO HIS ASN VAL MET ILE ASP HIS GLU HIS ARG LYS SEQRES 14 A 328 LEU ARG LEU ILE ASP TRP GLY LEU ALA GLU PHE TYR HIS SEQRES 15 A 328 PRO GLY GLN GLU TYR ASN VAL ARG VAL ALA SER ARG TYR SEQRES 16 A 328 PHE LYS GLY PRO GLU LEU LEU VAL ASP TYR GLN MET TYR SEQRES 17 A 328 ASP TYR SER LEU ASP MET TRP SER LEU GLY CYS MET LEU SEQRES 18 A 328 ALA SER MET ILE PHE ARG LYS GLU PRO PHE PHE HIS GLY SEQRES 19 A 328 HIS ASP ASN TYR ASP GLN LEU VAL ARG ILE ALA LYS VAL SEQRES 20 A 328 LEU GLY THR GLU ASP LEU TYR ASP TYR ILE ASP LYS TYR SEQRES 21 A 328 ASN ILE GLU LEU ASP PRO ARG PHE ASN ASP ILE LEU GLY SEQRES 22 A 328 ARG HIS SER ARG LYS ARG TRP GLU ARG PHE VAL HIS SER SEQRES 23 A 328 GLU ASN GLN HIS LEU VAL SER PRO GLU ALA LEU ASP PHE SEQRES 24 A 328 LEU ASP LYS LEU LEU ARG TYR ASP HIS GLN SER ARG LEU SEQRES 25 A 328 THR ALA ARG GLU ALA MET GLU HIS PRO TYR PHE TYR THR SEQRES 26 A 328 VAL VAL LYS HET ADP A 401 27 HET KEC A 402 14 HET ACT A 403 4 HET ACT A 404 4 HET ACT A 405 4 HET ACT A 406 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM KEC 2-(5-BROMANYL-6-CHLORANYL-1~{H}-INDOL-3-YL) HETNAM 2 KEC ETHANENITRILE HETNAM ACT ACETATE ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 KEC C10 H6 BR CL N2 FORMUL 4 ACT 4(C2 H3 O2 1-) FORMUL 8 HOH *207(H2 O) HELIX 1 AA1 ASP A 14 ARG A 19 1 6 HELIX 2 AA2 PRO A 20 ASP A 25 1 6 HELIX 3 AA3 TYR A 26 HIS A 29 5 4 HELIX 4 AA4 ASN A 35 ASP A 37 5 3 HELIX 5 AA5 PRO A 72 ALA A 76 5 5 HELIX 6 AA6 LYS A 77 ARG A 89 1 13 HELIX 7 AA7 ASP A 120 LEU A 128 1 9 HELIX 8 AA8 THR A 129 MET A 150 1 22 HELIX 9 AA9 LYS A 158 HIS A 160 5 3 HELIX 10 AB1 SER A 194 LYS A 198 5 5 HELIX 11 AB2 GLY A 199 VAL A 204 1 6 HELIX 12 AB3 TYR A 211 ARG A 228 1 18 HELIX 13 AB4 ASP A 237 GLY A 250 1 14 HELIX 14 AB5 GLY A 250 TYR A 261 1 12 HELIX 15 AB6 ASP A 266 ILE A 272 5 7 HELIX 16 AB7 ARG A 280 VAL A 285 5 6 HELIX 17 AB8 ASN A 289 VAL A 293 5 5 HELIX 18 AB9 SER A 294 LEU A 305 1 12 HELIX 19 AC1 ASP A 308 ARG A 312 5 5 HELIX 20 AC2 THR A 314 GLU A 320 1 7 HELIX 21 AC3 HIS A 321 TYR A 325 5 5 SHEET 1 AA1 5 TYR A 39 ARG A 47 0 SHEET 2 AA1 5 SER A 51 ASN A 58 -1 O VAL A 53 N GLY A 46 SHEET 3 AA1 5 LYS A 64 LEU A 70 -1 O ILE A 69 N GLU A 52 SHEET 4 AA1 5 PRO A 109 GLU A 114 -1 O PHE A 113 N VAL A 66 SHEET 5 AA1 5 LEU A 97 LYS A 102 -1 N ASP A 99 O VAL A 112 SHEET 1 AA2 2 ILE A 152 MET A 153 0 SHEET 2 AA2 2 GLU A 180 PHE A 181 -1 O GLU A 180 N MET A 153 SHEET 1 AA3 2 VAL A 162 ASP A 165 0 SHEET 2 AA3 2 LYS A 170 LEU A 173 -1 O LYS A 170 N ASP A 165 CISPEP 1 GLU A 230 PRO A 231 0 -0.89 CRYST1 58.343 45.842 63.266 90.00 111.38 90.00 P 1 21 1 2 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 0.017140 0.000000 0.006710 0.00000 SCALE2 0.000000 0.021814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016974 0.00000