HEADER CELL CYCLE 12-NOV-20 7DH3 TITLE THE CO-CRYSTAL STRUCTURE OF DYRK2 WITH A SMALL MOLECULE INHIBITOR 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 EC: 2.7.12.1; 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: DYRK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS KINASE, INHIBITOR, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR T.WEI,J.XIAO REVDAT 2 29-NOV-23 7DH3 1 REMARK REVDAT 1 17-NOV-21 7DH3 0 JRNL AUTH T.WEI,J.XIAO JRNL TITL THE CO-CRYSTAL STRUCTURE OF DYRK2 WITH A SMALL MOLECULE JRNL TITL 2 INHIBITOR 5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260: ??? 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 23127 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 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 4.6572 - 3.6977 0.93 2681 127 0.1624 0.1666 REMARK 3 2 3.6977 - 3.2306 0.79 2276 94 0.2054 0.2347 REMARK 3 3 3.2306 - 2.9354 1.00 2834 150 0.2153 0.2558 REMARK 3 4 2.9354 - 2.7251 1.00 2831 146 0.2323 0.2496 REMARK 3 5 2.7251 - 2.5644 1.00 2795 159 0.2374 0.2685 REMARK 3 6 2.5644 - 2.4360 1.00 2817 155 0.2449 0.2987 REMARK 3 7 2.4360 - 2.3300 1.00 2770 143 0.2487 0.3106 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.16 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7DH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23161 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 66.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.10200 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 REMARK 200 STARTING MODEL: 3K2L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.36 M-0.5 M SODIUM CITRATE TRIBASIC REMARK 280 DEHYDRATE, 0.01 M SODIUM BORATE, PH 7.5-9.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.22500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.22500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.22500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.28000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.41500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.22500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.28000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.41500 REMARK 290 SMTRY3 8 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 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 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 ARG A 221 -46.54 -156.60 REMARK 500 LYS A 226 140.22 -171.33 REMARK 500 HIS A 245 63.68 66.77 REMARK 500 ASN A 255 54.67 -92.51 REMARK 500 LYS A 257 -113.33 33.53 REMARK 500 SER A 305 -147.43 -96.59 REMARK 500 ASP A 348 41.29 -150.52 REMARK 500 ASP A 368 74.58 58.29 REMARK 500 GLN A 384 151.84 72.29 REMARK 500 SER A 474 131.30 -35.41 REMARK 500 ASP A 505 102.05 -54.07 REMARK 500 LEU A 516 31.35 -92.91 REMARK 500 LEU A 535 -156.43 -103.84 REMARK 500 ARG A 537 -145.48 -134.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DH3 A 213 538 UNP Q92630 DYRK2_HUMAN 213 538 SEQRES 1 A 326 VAL PRO HIS ASP HIS VAL ALA TYR ARG TYR GLU VAL LEU SEQRES 2 A 326 LYS VAL ILE GLY LYS GLY SER PHE GLY GLN VAL VAL LYS SEQRES 3 A 326 ALA TYR ASP HIS LYS VAL HIS GLN HIS VAL ALA LEU LYS SEQRES 4 A 326 MET VAL ARG ASN GLU LYS ARG PHE HIS ARG GLN ALA ALA SEQRES 5 A 326 GLU GLU ILE ARG ILE LEU GLU HIS LEU ARG LYS GLN ASP SEQRES 6 A 326 LYS ASP ASN THR MET ASN VAL ILE HIS MET LEU GLU ASN SEQRES 7 A 326 PHE THR PHE ARG ASN HIS ILE CYS MET THR PHE GLU LEU SEQRES 8 A 326 LEU SER MET ASN LEU TYR GLU LEU ILE LYS LYS ASN LYS SEQRES 9 A 326 PHE GLN GLY PHE SER LEU PRO LEU VAL ARG LYS PHE ALA SEQRES 10 A 326 HIS SER ILE LEU GLN CYS LEU ASP ALA LEU HIS LYS ASN SEQRES 11 A 326 ARG ILE ILE HIS CYS ASP LEU LYS PRO GLU ASN ILE LEU SEQRES 12 A 326 LEU LYS GLN GLN GLY ARG SER GLY ILE LYS VAL ILE ASP SEQRES 13 A 326 PHE GLY SER SER CYS TYR GLU HIS GLN ARG VAL TYR THR SEQRES 14 A 326 PTR ILE GLN SER ARG PHE TYR ARG ALA PRO GLU VAL ILE SEQRES 15 A 326 LEU GLY ALA ARG TYR GLY MET PRO ILE ASP MET TRP SER SEQRES 16 A 326 LEU GLY CYS ILE LEU ALA GLU LEU LEU THR GLY TYR PRO SEQRES 17 A 326 LEU LEU PRO GLY GLU ASP GLU GLY ASP GLN LEU ALA CYS SEQRES 18 A 326 MET ILE GLU LEU LEU GLY MET PRO SER GLN LYS LEU LEU SEQRES 19 A 326 ASP ALA SER LYS ARG ALA LYS ASN PHE VAL SER SEP LYS SEQRES 20 A 326 GLY TYR PRO ARG TYR CYS THR VAL THR THR LEU SER ASP SEQRES 21 A 326 GLY SER VAL VAL LEU ASN GLY GLY ARG SER ARG ARG GLY SEQRES 22 A 326 LYS LEU ARG GLY PRO PRO GLU SER ARG GLU TRP GLY ASN SEQRES 23 A 326 ALA LEU LYS GLY CYS ASP ASP PRO LEU PHE LEU ASP PHE SEQRES 24 A 326 LEU LYS GLN CYS LEU GLU TRP ASP PRO ALA VAL ARG MET SEQRES 25 A 326 THR PRO GLY GLN ALA LEU ARG HIS PRO TRP LEU ARG ARG SEQRES 26 A 326 ARG MODRES 7DH3 PTR A 382 TYR MODIFIED RESIDUE MODRES 7DH3 SEP A 458 SER MODIFIED RESIDUE HET PTR A 382 16 HET SEP A 458 10 HET H7C A 601 25 HETNAM PTR O-PHOSPHOTYROSINE HETNAM SEP PHOSPHOSERINE HETNAM H7C 2,7-DIMETHOXY-9-PIPERIDIN-4-YLSULFANYL-ACRIDINE HETSYN PTR PHOSPHONOTYROSINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 H7C C20 H22 N2 O2 S FORMUL 3 HOH *64(H2 O) HELIX 1 AA1 PHE A 259 LYS A 275 1 17 HELIX 2 AA2 ASN A 307 ASN A 315 1 9 HELIX 3 AA3 SER A 321 ASN A 342 1 22 HELIX 4 AA4 LYS A 350 GLU A 352 5 3 HELIX 5 AA5 SER A 385 ARG A 389 5 5 HELIX 6 AA6 ALA A 390 GLY A 396 1 7 HELIX 7 AA7 MET A 401 GLY A 418 1 18 HELIX 8 AA8 ASP A 426 GLY A 439 1 14 HELIX 9 AA9 SER A 442 ALA A 448 1 7 HELIX 10 AB1 ARG A 451 PHE A 455 5 5 HELIX 11 AB2 GLU A 495 LEU A 500 1 6 HELIX 12 AB3 ASP A 505 LEU A 516 1 12 HELIX 13 AB4 THR A 525 ARG A 531 1 7 SHEET 1 AA1 6 HIS A 217 VAL A 218 0 SHEET 2 AA1 6 TYR A 222 GLY A 231 -1 O TYR A 222 N VAL A 218 SHEET 3 AA1 6 GLY A 234 ASP A 241 -1 O VAL A 236 N GLY A 229 SHEET 4 AA1 6 GLN A 246 VAL A 253 -1 O LEU A 250 N VAL A 237 SHEET 5 AA1 6 ILE A 297 PHE A 301 -1 O MET A 299 N LYS A 251 SHEET 6 AA1 6 MET A 287 THR A 292 -1 N PHE A 291 O CYS A 298 SHEET 1 AA2 2 ILE A 344 ILE A 345 0 SHEET 2 AA2 2 CYS A 373 TYR A 374 -1 O CYS A 373 N ILE A 345 SHEET 1 AA3 2 ILE A 354 LEU A 356 0 SHEET 2 AA3 2 ILE A 364 VAL A 366 -1 O LYS A 365 N LEU A 355 SHEET 1 AA4 2 VAL A 467 THR A 469 0 SHEET 2 AA4 2 VAL A 475 LEU A 477 -1 O VAL A 476 N THR A 468 SHEET 1 AA5 2 GLY A 480 ARG A 481 0 SHEET 2 AA5 2 LEU A 487 ARG A 488 -1 O ARG A 488 N GLY A 480 LINK C THR A 381 N PTR A 382 1555 1555 1.33 LINK C PTR A 382 N ILE A 383 1555 1555 1.33 LINK C SER A 457 N SEP A 458 1555 1555 1.33 LINK C SEP A 458 N LYS A 459 1555 1555 1.33 CRYST1 64.560 128.830 132.450 90.00 90.00 90.00 C 2 2 21 8 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 0.015489 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007550 0.00000