HEADER TRANSFERASE 26-JUL-20 7CMB TITLE CRYSTAL STRUCTURE OF PAK4 IN COMPLEX WITH INHIBITOR 41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PAK 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PAK4 KINASE DOMAIN; COMPND 5 SYNONYM: P21-ACTIVATED KINASE 4,PAK-4; COMPND 6 EC: 2.7.11.1; COMPND 7 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: PAK4, KIAA1142; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSUMOH10 KEYWDS ATP BINDING POCKET, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ZHAO,H.LI REVDAT 3 13-NOV-24 7CMB 1 REMARK REVDAT 2 29-NOV-23 7CMB 1 REMARK REVDAT 1 28-JUL-21 7CMB 0 JRNL AUTH P.SONG,F.ZHAO,M.CHENG JRNL TITL DISCOVERY OF 6-ETHYNYL-1H-INDOLE-3-CARBOXAMIDE DERIVATIVES JRNL TITL 2 AS HIGHLY POTENT AND SELECTIVE P21-ACTIVATED KINASE 4 (PAK4) JRNL TITL 3 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3247 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 621 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 26.0630 - 4.1108 0.99 3058 162 0.1855 0.2375 REMARK 3 2 4.1108 - 3.2649 1.00 2881 158 0.2167 0.2372 REMARK 3 3 3.2649 - 2.8528 1.00 2856 147 0.2426 0.2858 REMARK 3 4 2.8528 - 2.5922 0.99 2810 154 0.2547 0.3300 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.00 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 7CMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12343 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.592 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 1.08500 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: 5XVF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M TRIS PH REMARK 280 8.5, 25% PEG3350, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 88.45050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.26100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.26100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.22525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.26100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.26100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.67575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.26100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.26100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.22525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.26100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.26100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 132.67575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.45050 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 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 THR A 590 REMARK 465 ARG A 591 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 GLU A 329 -161.16 -127.73 REMARK 500 SER A 331 69.47 -63.86 REMARK 500 ASP A 440 40.08 -155.68 REMARK 500 ASP A 458 70.68 58.57 REMARK 500 ASN A 588 -126.39 -132.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CMB A 300 591 UNP O96013 PAK4_HUMAN 300 591 SEQADV 7CMB SER A 299 UNP O96013 EXPRESSION TAG SEQRES 1 A 293 SER SER HIS GLU GLN PHE ARG ALA ALA LEU GLN LEU VAL SEQRES 2 A 293 VAL ASP PRO GLY ASP PRO ARG SER TYR LEU ASP ASN PHE SEQRES 3 A 293 ILE LYS ILE GLY GLU GLY SER THR GLY ILE VAL CYS ILE SEQRES 4 A 293 ALA THR VAL ARG SER SER GLY LYS LEU VAL ALA VAL LYS SEQRES 5 A 293 LYS MET ASP LEU ARG LYS GLN GLN ARG ARG GLU LEU LEU SEQRES 6 A 293 PHE ASN GLU VAL VAL ILE MET ARG ASP TYR GLN HIS GLU SEQRES 7 A 293 ASN VAL VAL GLU MET TYR ASN SER TYR LEU VAL GLY ASP SEQRES 8 A 293 GLU LEU TRP VAL VAL MET GLU PHE LEU GLU GLY GLY ALA SEQRES 9 A 293 LEU THR ASP ILE VAL THR HIS THR ARG MET ASN GLU GLU SEQRES 10 A 293 GLN ILE ALA ALA VAL CYS LEU ALA VAL LEU GLN ALA LEU SEQRES 11 A 293 SER VAL LEU HIS ALA GLN GLY VAL ILE HIS ARG ASP ILE SEQRES 12 A 293 LYS SER ASP SER ILE LEU LEU THR HIS ASP GLY ARG VAL SEQRES 13 A 293 LYS LEU SER ASP PHE GLY PHE CYS ALA GLN VAL SER LYS SEQRES 14 A 293 GLU VAL PRO ARG ARG LYS SEP LEU VAL GLY THR PRO TYR SEQRES 15 A 293 TRP MET ALA PRO GLU LEU ILE SER ARG LEU PRO TYR GLY SEQRES 16 A 293 PRO GLU VAL ASP ILE TRP SER LEU GLY ILE MET VAL ILE SEQRES 17 A 293 GLU MET VAL ASP GLY GLU PRO PRO TYR PHE ASN GLU PRO SEQRES 18 A 293 PRO LEU LYS ALA MET LYS MET ILE ARG ASP ASN LEU PRO SEQRES 19 A 293 PRO ARG LEU LYS ASN LEU HIS LYS VAL SER PRO SER LEU SEQRES 20 A 293 LYS GLY PHE LEU ASP ARG LEU LEU VAL ARG ASP PRO ALA SEQRES 21 A 293 GLN ARG ALA THR ALA ALA GLU LEU LEU LYS HIS PRO PHE SEQRES 22 A 293 LEU ALA LYS ALA GLY PRO PRO ALA SER ILE VAL PRO LEU SEQRES 23 A 293 MET ARG GLN ASN ARG THR ARG MODRES 7CMB SEP A 474 SER MODIFIED RESIDUE HET SEP A 474 10 HET G5X A 601 28 HETNAM SEP PHOSPHOSERINE HETNAM G5X 1-(2-AZANYLPYRIMIDIN-4-YL)-6-[2-(1-OXIDANYLCYCLOHEXYL) HETNAM 2 G5X ETHYNYL]INDOLE-3-CARBOXAMIDE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 G5X C21 H21 N5 O2 FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 SER A 299 LEU A 310 1 12 HELIX 2 AA2 ASP A 316 SER A 319 5 4 HELIX 3 AA3 ARG A 359 MET A 370 1 12 HELIX 4 AA4 LEU A 403 THR A 410 1 8 HELIX 5 AA5 ASN A 413 GLN A 434 1 22 HELIX 6 AA6 LYS A 442 ASP A 444 5 3 HELIX 7 AA7 THR A 478 MET A 482 5 5 HELIX 8 AA8 ALA A 483 SER A 488 1 6 HELIX 9 AA9 PRO A 494 GLY A 511 1 18 HELIX 10 AB1 PRO A 519 ASN A 530 1 12 HELIX 11 AB2 ASN A 537 VAL A 541 5 5 HELIX 12 AB3 SER A 542 ARG A 551 1 10 HELIX 13 AB4 THR A 562 LEU A 567 1 6 HELIX 14 AB5 LYS A 568 ALA A 575 5 8 HELIX 15 AB6 PRO A 577 VAL A 582 1 6 HELIX 16 AB7 PRO A 583 MET A 585 5 3 SHEET 1 AA1 5 LEU A 321 GLY A 328 0 SHEET 2 AA1 5 GLY A 333 VAL A 340 -1 O VAL A 335 N ILE A 327 SHEET 3 AA1 5 LEU A 346 ASP A 353 -1 O LYS A 351 N ILE A 334 SHEET 4 AA1 5 GLU A 390 GLU A 396 -1 O LEU A 391 N MET A 352 SHEET 5 AA1 5 MET A 381 VAL A 387 -1 N TYR A 385 O TRP A 392 SHEET 1 AA2 3 GLY A 401 ALA A 402 0 SHEET 2 AA2 3 ILE A 446 LEU A 448 -1 O LEU A 448 N GLY A 401 SHEET 3 AA2 3 VAL A 454 LEU A 456 -1 O LYS A 455 N LEU A 447 SHEET 1 AA3 2 VAL A 436 ILE A 437 0 SHEET 2 AA3 2 ALA A 463 GLN A 464 -1 O ALA A 463 N ILE A 437 LINK C LYS A 473 N SEP A 474 1555 1555 1.33 LINK C SEP A 474 N LEU A 475 1555 1555 1.33 CRYST1 64.522 64.522 176.901 90.00 90.00 90.00 P 41 21 2 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 0.015499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005653 0.00000