HEADER TRANSFERASE 07-APR-20 6YM5 TITLE CRYSTAL STRUCTURE OF BAY-091 WITH PIP4K2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE TYPE-2 ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 1-PHOSPHATIDYLINOSITOL 5-PHOSPHATE 4-KINASE 2-ALPHA, COMPND 5 DIPHOSPHOINOSITIDE KINASE 2-ALPHA,PIP5KIII,PHOSPHATIDYLINOSITOL 5- COMPND 6 PHOSPHATE 4-KINASE TYPE II ALPHA,PIP4KII-ALPHA,PTDINS(4)P-5-KINASE B COMPND 7 ISOFORM,PTDINS(4)P-5-KINASE C ISOFORM,PTDINS(5)P-4-KINASE ISOFORM 2- COMPND 8 ALPHA; COMPND 9 EC: 2.7.1.149; COMPND 10 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: PIP4K2A, PIP5K2, PIP5K2A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PIP4K2A, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.HOLTON,L.WORTMANN,N.BRAEUER,H.IRLBACHER,J.WEISKE,C.LECHNER, AUTHOR 2 R.MEIER,V.PUETTER,C.CHRIST,T.TER LAAK,P.LIENAU,R.LESCHE,B.NICKE, AUTHOR 3 M.BAUSER,A.HAEGEBARTH,F.VON NUSSBAUM,D.MUMBERG,C.LEMOS REVDAT 4 24-JAN-24 6YM5 1 REMARK REVDAT 3 24-NOV-21 6YM5 1 JRNL REVDAT 2 17-NOV-21 6YM5 1 JRNL REVDAT 1 14-APR-21 6YM5 0 JRNL AUTH L.WORTMANN,N.BRAUER,S.J.HOLTON,H.IRLBACHER,J.WEISKE, JRNL AUTH 2 C.LECHNER,R.MEIER,J.KAREN,C.B.SIOBERG,V.PUTTER,C.D.CHRIST, JRNL AUTH 3 A.TER LAAK,P.LIENAU,R.LESCHE,B.NICKE,S.H.CHEUNG,M.BAUSER, JRNL AUTH 4 A.HAEGEBARTH,F.VON NUSSBAUM,D.MUMBERG,C.LEMOS JRNL TITL DISCOVERY AND CHARACTERIZATION OF THE POTENT AND HIGHLY JRNL TITL 2 SELECTIVE 1,7-NAPHTHYRIDINE-BASED INHIBITORS BAY-091 AND JRNL TITL 3 BAY-297 OF THE KINASE PIP4K2A. JRNL REF J.MED.CHEM. V. 64 15883 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34699202 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01245 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 104.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 27527 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1419 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2023 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.72000 REMARK 3 B22 (A**2) : 1.00000 REMARK 3 B33 (A**2) : 1.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.454 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.361 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5413 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4931 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7313 ; 1.662 ; 1.663 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11474 ; 1.279 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 623 ; 8.047 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;32.807 ;23.087 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 972 ;15.889 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.949 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 675 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5939 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1112 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 28 A 1002 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8030 5.0080 -6.2090 REMARK 3 T TENSOR REMARK 3 T11: 0.0534 T22: 0.2281 REMARK 3 T33: 0.0213 T12: -0.0080 REMARK 3 T13: 0.0126 T23: -0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.8690 L22: 1.4239 REMARK 3 L33: 2.7134 L12: 0.1739 REMARK 3 L13: -0.5524 L23: -1.1370 REMARK 3 S TENSOR REMARK 3 S11: -0.0218 S12: 0.1607 S13: 0.1304 REMARK 3 S21: -0.1420 S22: 0.0109 S23: -0.0223 REMARK 3 S31: -0.0299 S32: -0.1458 S33: 0.0109 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 29 B 1002 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9260 -4.0630 44.5110 REMARK 3 T TENSOR REMARK 3 T11: 0.0618 T22: 0.1904 REMARK 3 T33: 0.0104 T12: 0.0010 REMARK 3 T13: -0.0081 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 1.4550 L22: 0.8910 REMARK 3 L33: 3.4476 L12: -0.0855 REMARK 3 L13: -0.7274 L23: 0.2406 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: -0.2327 S13: 0.0128 REMARK 3 S21: 0.1867 S22: -0.0125 S23: -0.0598 REMARK 3 S31: 0.0098 S32: 0.1224 S33: 0.0620 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6YM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-18 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9919 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 : 29002 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 104.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 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: MOLREP REMARK 200 STARTING MODEL: 2YBX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 200MM MAGNESIUM FORMATE, REMARK 280 25% GYLCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 49.69400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 SER A 19 REMARK 465 SER A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 22 REMARK 465 ASP A 23 REMARK 465 LEU A 24 REMARK 465 GLY A 25 REMARK 465 THR A 26 REMARK 465 GLU A 27 REMARK 465 ASP A 125 REMARK 465 SER A 126 REMARK 465 GLN A 127 REMARK 465 ALA A 128 REMARK 465 ARG A 129 REMARK 465 SER A 130 REMARK 465 GLY A 131 REMARK 465 ALA A 132 REMARK 465 THR A 216 REMARK 465 VAL A 217 REMARK 465 ALA A 218 REMARK 465 GLU A 294 REMARK 465 GLU A 295 REMARK 465 ASN A 296 REMARK 465 ASP A 297 REMARK 465 GLY A 298 REMARK 465 GLU A 299 REMARK 465 GLU A 300 REMARK 465 GLU A 301 REMARK 465 GLY A 302 REMARK 465 GLU A 303 REMARK 465 SER A 304 REMARK 465 ASP A 305 REMARK 465 GLY A 306 REMARK 465 THR A 307 REMARK 465 HIS A 308 REMARK 465 PRO A 309 REMARK 465 VAL A 310 REMARK 465 GLY A 311 REMARK 465 THR A 312 REMARK 465 PRO A 313 REMARK 465 PRO A 314 REMARK 465 ASP A 315 REMARK 465 SER A 316 REMARK 465 PRO A 317 REMARK 465 GLY A 318 REMARK 465 ASN A 319 REMARK 465 THR A 320 REMARK 465 LEU A 321 REMARK 465 ASN A 322 REMARK 465 SER A 323 REMARK 465 SER A 324 REMARK 465 PRO A 325 REMARK 465 ASP A 365 REMARK 465 ALA A 366 REMARK 465 LYS A 367 REMARK 465 LYS A 368 REMARK 465 LYS A 369 REMARK 465 ALA A 370 REMARK 465 ALA A 371 REMARK 465 HIS A 372 REMARK 465 ALA A 373 REMARK 465 ALA A 374 REMARK 465 LYS A 375 REMARK 465 THR A 376 REMARK 465 VAL A 377 REMARK 465 LYS A 378 REMARK 465 HIS A 379 REMARK 465 GLY A 380 REMARK 465 ALA A 381 REMARK 465 GLY A 382 REMARK 465 ALA A 383 REMARK 465 GLU A 384 REMARK 465 ILE A 385 REMARK 465 SER A 386 REMARK 465 THR A 387 REMARK 465 MET B 12 REMARK 465 HIS B 13 REMARK 465 HIS B 14 REMARK 465 HIS B 15 REMARK 465 HIS B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 SER B 19 REMARK 465 SER B 20 REMARK 465 GLY B 21 REMARK 465 VAL B 22 REMARK 465 ASP B 23 REMARK 465 LEU B 24 REMARK 465 GLY B 25 REMARK 465 THR B 26 REMARK 465 GLU B 27 REMARK 465 ASN B 28 REMARK 465 ASP B 125 REMARK 465 SER B 126 REMARK 465 GLN B 127 REMARK 465 ALA B 128 REMARK 465 ARG B 129 REMARK 465 SER B 130 REMARK 465 GLY B 131 REMARK 465 ALA B 132 REMARK 465 ARG B 133 REMARK 465 GLU B 287 REMARK 465 GLN B 288 REMARK 465 GLU B 289 REMARK 465 GLU B 290 REMARK 465 VAL B 291 REMARK 465 GLU B 292 REMARK 465 CYS B 293 REMARK 465 GLU B 294 REMARK 465 GLU B 295 REMARK 465 ASN B 296 REMARK 465 ASP B 297 REMARK 465 GLY B 298 REMARK 465 GLU B 299 REMARK 465 GLU B 300 REMARK 465 GLU B 301 REMARK 465 GLY B 302 REMARK 465 GLU B 303 REMARK 465 SER B 304 REMARK 465 ASP B 305 REMARK 465 GLY B 306 REMARK 465 THR B 307 REMARK 465 HIS B 308 REMARK 465 PRO B 309 REMARK 465 VAL B 310 REMARK 465 GLY B 311 REMARK 465 THR B 312 REMARK 465 PRO B 313 REMARK 465 PRO B 314 REMARK 465 ASP B 315 REMARK 465 SER B 316 REMARK 465 PRO B 317 REMARK 465 GLY B 318 REMARK 465 ASN B 319 REMARK 465 THR B 320 REMARK 465 LEU B 321 REMARK 465 ASN B 322 REMARK 465 SER B 323 REMARK 465 SER B 324 REMARK 465 PRO B 325 REMARK 465 PRO B 326 REMARK 465 LEU B 327 REMARK 465 LYS B 367 REMARK 465 LYS B 368 REMARK 465 LYS B 369 REMARK 465 ALA B 370 REMARK 465 ALA B 371 REMARK 465 HIS B 372 REMARK 465 ALA B 373 REMARK 465 ALA B 374 REMARK 465 LYS B 375 REMARK 465 THR B 376 REMARK 465 VAL B 377 REMARK 465 LYS B 378 REMARK 465 HIS B 379 REMARK 465 GLY B 380 REMARK 465 ALA B 381 REMARK 465 GLY B 382 REMARK 465 ALA B 383 REMARK 465 GLU B 384 REMARK 465 ILE B 385 REMARK 465 SER B 386 REMARK 465 THR B 387 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 203 -56.26 -129.89 REMARK 500 LYS A 213 -54.02 -125.67 REMARK 500 LYS A 270 35.39 73.06 REMARK 500 GLU A 345 -33.22 -38.80 REMARK 500 PHD A 359 64.38 67.39 REMARK 500 PHD A 359 60.54 67.39 REMARK 500 LEU A 361 58.25 -94.17 REMARK 500 LEU A 361 58.25 -94.25 REMARK 500 CYS B 94 60.67 38.90 REMARK 500 THR B 117 -44.69 -138.99 REMARK 500 ARG B 203 -64.24 -126.27 REMARK 500 ALA B 218 97.41 -50.15 REMARK 500 LYS B 270 34.36 72.83 REMARK 500 ILE B 336 -64.08 -95.46 REMARK 500 PHD B 359 64.17 62.19 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 PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OZ5 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OZ5 B 502 DBREF 6YM5 A 35 405 UNP P48426 PI42A_HUMAN 35 405 DBREF 6YM5 B 35 405 UNP P48426 PI42A_HUMAN 35 405 SEQADV 6YM5 MET A 12 UNP P48426 INITIATING METHIONINE SEQADV 6YM5 HIS A 13 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS A 14 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS A 15 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS A 16 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS A 17 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS A 18 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER A 19 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER A 20 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLY A 21 UNP P48426 EXPRESSION TAG SEQADV 6YM5 VAL A 22 UNP P48426 EXPRESSION TAG SEQADV 6YM5 ASP A 23 UNP P48426 EXPRESSION TAG SEQADV 6YM5 LEU A 24 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLY A 25 UNP P48426 EXPRESSION TAG SEQADV 6YM5 THR A 26 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLU A 27 UNP P48426 EXPRESSION TAG SEQADV 6YM5 ASN A 28 UNP P48426 EXPRESSION TAG SEQADV 6YM5 LEU A 29 UNP P48426 EXPRESSION TAG SEQADV 6YM5 TYR A 30 UNP P48426 EXPRESSION TAG SEQADV 6YM5 PHE A 31 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLN A 32 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER A 33 UNP P48426 EXPRESSION TAG SEQADV 6YM5 MET A 34 UNP P48426 EXPRESSION TAG SEQADV 6YM5 MET B 12 UNP P48426 INITIATING METHIONINE SEQADV 6YM5 HIS B 13 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS B 14 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS B 15 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS B 16 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS B 17 UNP P48426 EXPRESSION TAG SEQADV 6YM5 HIS B 18 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER B 19 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER B 20 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLY B 21 UNP P48426 EXPRESSION TAG SEQADV 6YM5 VAL B 22 UNP P48426 EXPRESSION TAG SEQADV 6YM5 ASP B 23 UNP P48426 EXPRESSION TAG SEQADV 6YM5 LEU B 24 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLY B 25 UNP P48426 EXPRESSION TAG SEQADV 6YM5 THR B 26 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLU B 27 UNP P48426 EXPRESSION TAG SEQADV 6YM5 ASN B 28 UNP P48426 EXPRESSION TAG SEQADV 6YM5 LEU B 29 UNP P48426 EXPRESSION TAG SEQADV 6YM5 TYR B 30 UNP P48426 EXPRESSION TAG SEQADV 6YM5 PHE B 31 UNP P48426 EXPRESSION TAG SEQADV 6YM5 GLN B 32 UNP P48426 EXPRESSION TAG SEQADV 6YM5 SER B 33 UNP P48426 EXPRESSION TAG SEQADV 6YM5 MET B 34 UNP P48426 EXPRESSION TAG SEQRES 1 A 394 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 394 GLY THR GLU ASN LEU TYR PHE GLN SER MET ASP PRO LEU SEQRES 3 A 394 LEU SER VAL LEU MET TRP GLY VAL ASN HIS SER ILE ASN SEQRES 4 A 394 GLU LEU SER HIS VAL GLN ILE PRO VAL MET LEU MET PRO SEQRES 5 A 394 ASP ASP PHE LYS ALA TYR SER LYS ILE LYS VAL ASP ASN SEQRES 6 A 394 HIS LEU PHE ASN LYS GLU ASN MET PRO SER HIS PHE LYS SEQRES 7 A 394 PHE LYS GLU TYR CYS PRO MET VAL PHE ARG ASN LEU ARG SEQRES 8 A 394 GLU ARG PHE GLY ILE ASP ASP GLN ASP PHE GLN ASN SER SEQRES 9 A 394 LEU THR ARG SER ALA PRO LEU PRO ASN ASP SER GLN ALA SEQRES 10 A 394 ARG SER GLY ALA ARG PHE HIS THR SER TYR ASP LYS ARG SEQRES 11 A 394 TYR ILE ILE LYS THR ILE THR SER GLU ASP VAL ALA GLU SEQRES 12 A 394 MET HIS ASN ILE LEU LYS LYS TYR HIS GLN TYR ILE VAL SEQRES 13 A 394 GLU CYS HIS GLY ILE THR LEU LEU PRO GLN PHE LEU GLY SEQRES 14 A 394 MET TYR ARG LEU ASN VAL ASP GLY VAL GLU ILE TYR VAL SEQRES 15 A 394 ILE VAL THR ARG ASN VAL PHE SER HIS ARG LEU SER VAL SEQRES 16 A 394 TYR ARG LYS TYR ASP LEU LYS GLY SER THR VAL ALA ARG SEQRES 17 A 394 GLU ALA SER ASP LYS GLU LYS ALA LYS GLU LEU PRO THR SEQRES 18 A 394 LEU LYS ASP ASN ASP PHE ILE ASN GLU GLY GLN LYS ILE SEQRES 19 A 394 TYR ILE ASP ASP ASN ASN LYS LYS VAL PHE LEU GLU LYS SEQRES 20 A 394 LEU LYS LYS ASP VAL GLU PHE LEU ALA GLN LEU LYS LEU SEQRES 21 A 394 MET ASP TYR SER LEU LEU VAL GLY ILE HIS ASP VAL GLU SEQRES 22 A 394 ARG ALA GLU GLN GLU GLU VAL GLU CYS GLU GLU ASN ASP SEQRES 23 A 394 GLY GLU GLU GLU GLY GLU SER ASP GLY THR HIS PRO VAL SEQRES 24 A 394 GLY THR PRO PRO ASP SER PRO GLY ASN THR LEU ASN SER SEQRES 25 A 394 SER PRO PRO LEU ALA PRO GLY GLU PHE ASP PRO ASN ILE SEQRES 26 A 394 ASP VAL TYR GLY ILE LYS CYS HIS GLU ASN SER PRO ARG SEQRES 27 A 394 LYS GLU VAL TYR PHE MET ALA ILE ILE PHD ILE LEU THR SEQRES 28 A 394 HIS TYR ASP ALA LYS LYS LYS ALA ALA HIS ALA ALA LYS SEQRES 29 A 394 THR VAL LYS HIS GLY ALA GLY ALA GLU ILE SER THR VAL SEQRES 30 A 394 ASN PRO GLU GLN TYR SER LYS ARG PHE LEU ASP PHE ILE SEQRES 31 A 394 GLY HIS ILE LEU SEQRES 1 B 394 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 394 GLY THR GLU ASN LEU TYR PHE GLN SER MET ASP PRO LEU SEQRES 3 B 394 LEU SER VAL LEU MET TRP GLY VAL ASN HIS SER ILE ASN SEQRES 4 B 394 GLU LEU SER HIS VAL GLN ILE PRO VAL MET LEU MET PRO SEQRES 5 B 394 ASP ASP PHE LYS ALA TYR SER LYS ILE LYS VAL ASP ASN SEQRES 6 B 394 HIS LEU PHE ASN LYS GLU ASN MET PRO SER HIS PHE LYS SEQRES 7 B 394 PHE LYS GLU TYR CYS PRO MET VAL PHE ARG ASN LEU ARG SEQRES 8 B 394 GLU ARG PHE GLY ILE ASP ASP GLN ASP PHE GLN ASN SER SEQRES 9 B 394 LEU THR ARG SER ALA PRO LEU PRO ASN ASP SER GLN ALA SEQRES 10 B 394 ARG SER GLY ALA ARG PHE HIS THR SER TYR ASP LYS ARG SEQRES 11 B 394 TYR ILE ILE LYS THR ILE THR SER GLU ASP VAL ALA GLU SEQRES 12 B 394 MET HIS ASN ILE LEU LYS LYS TYR HIS GLN TYR ILE VAL SEQRES 13 B 394 GLU CYS HIS GLY ILE THR LEU LEU PRO GLN PHE LEU GLY SEQRES 14 B 394 MET TYR ARG LEU ASN VAL ASP GLY VAL GLU ILE TYR VAL SEQRES 15 B 394 ILE VAL THR ARG ASN VAL PHE SER HIS ARG LEU SER VAL SEQRES 16 B 394 TYR ARG LYS TYR ASP LEU LYS GLY SER THR VAL ALA ARG SEQRES 17 B 394 GLU ALA SER ASP LYS GLU LYS ALA LYS GLU LEU PRO THR SEQRES 18 B 394 LEU LYS ASP ASN ASP PHE ILE ASN GLU GLY GLN LYS ILE SEQRES 19 B 394 TYR ILE ASP ASP ASN ASN LYS LYS VAL PHE LEU GLU LYS SEQRES 20 B 394 LEU LYS LYS ASP VAL GLU PHE LEU ALA GLN LEU LYS LEU SEQRES 21 B 394 MET ASP TYR SER LEU LEU VAL GLY ILE HIS ASP VAL GLU SEQRES 22 B 394 ARG ALA GLU GLN GLU GLU VAL GLU CYS GLU GLU ASN ASP SEQRES 23 B 394 GLY GLU GLU GLU GLY GLU SER ASP GLY THR HIS PRO VAL SEQRES 24 B 394 GLY THR PRO PRO ASP SER PRO GLY ASN THR LEU ASN SER SEQRES 25 B 394 SER PRO PRO LEU ALA PRO GLY GLU PHE ASP PRO ASN ILE SEQRES 26 B 394 ASP VAL TYR GLY ILE LYS CYS HIS GLU ASN SER PRO ARG SEQRES 27 B 394 LYS GLU VAL TYR PHE MET ALA ILE ILE PHD ILE LEU THR SEQRES 28 B 394 HIS TYR ASP ALA LYS LYS LYS ALA ALA HIS ALA ALA LYS SEQRES 29 B 394 THR VAL LYS HIS GLY ALA GLY ALA GLU ILE SER THR VAL SEQRES 30 B 394 ASN PRO GLU GLN TYR SER LYS ARG PHE LEU ASP PHE ILE SEQRES 31 B 394 GLY HIS ILE LEU MODRES 6YM5 PHD A 359 ASP MODIFIED RESIDUE MODRES 6YM5 PHD B 359 ASP MODIFIED RESIDUE HET PHD A 359 12 HET PHD B 359 12 HET PO4 A 501 5 HET OZ5 A 502 33 HET PO4 B 501 5 HET OZ5 B 502 33 HETNAM PHD ASPARTYL PHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM OZ5 (2~{R})-2-[[3-CYANO-2-[4-(2-FLUORANYL-3-METHYL-PHENYL) HETNAM 2 OZ5 PHENYL]-1,7-NAPHTHYRIDIN-4-YL]AMINO]BUTANOIC ACID FORMUL 1 PHD 2(C4 H8 N O7 P) FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 OZ5 2(C26 H21 F N4 O2) FORMUL 7 HOH *126(H2 O) HELIX 1 AA1 ASP A 35 SER A 53 1 19 HELIX 2 AA2 MET A 62 LYS A 67 5 6 HELIX 3 AA3 CYS A 94 PHE A 105 1 12 HELIX 4 AA4 ASP A 108 ARG A 118 1 11 HELIX 5 AA5 THR A 148 CYS A 169 1 22 HELIX 6 AA6 SER A 222 ALA A 227 1 6 HELIX 7 AA7 ASP A 235 GLU A 241 1 7 HELIX 8 AA8 ASP A 248 LEU A 269 1 22 HELIX 9 AA9 VAL A 283 VAL A 291 1 9 HELIX 10 AB1 ASN A 389 LEU A 405 1 17 HELIX 11 AB2 ASP B 35 SER B 53 1 19 HELIX 12 AB3 MET B 62 LYS B 67 5 6 HELIX 13 AB4 CYS B 94 PHE B 105 1 12 HELIX 14 AB5 ASP B 108 LEU B 116 1 9 HELIX 15 AB6 THR B 148 CYS B 169 1 22 HELIX 16 AB7 SER B 222 LYS B 228 1 7 HELIX 17 AB8 LYS B 234 GLU B 241 1 8 HELIX 18 AB9 ASP B 248 LEU B 269 1 22 HELIX 19 AC1 ASN B 389 LEU B 405 1 17 SHEET 1 AA113 LEU A 122 PRO A 123 0 SHEET 2 AA113 HIS A 135 THR A 136 -1 O THR A 136 N LEU A 122 SHEET 3 AA113 TYR A 142 ILE A 147 -1 O ILE A 144 N HIS A 135 SHEET 4 AA113 VAL A 189 ARG A 197 -1 O THR A 196 N ILE A 143 SHEET 5 AA113 PHE A 178 VAL A 186 -1 N LEU A 184 O ILE A 191 SHEET 6 AA113 HIS A 87 TYR A 93 -1 N LYS A 91 O ARG A 183 SHEET 7 AA113 TYR A 69 HIS A 77 -1 N ILE A 72 O PHE A 90 SHEET 8 AA113 TYR B 69 HIS B 77 -1 O LYS B 73 N LYS A 73 SHEET 9 AA113 HIS B 87 TYR B 93 -1 O PHE B 88 N VAL B 74 SHEET 10 AA113 PHE B 178 VAL B 186 -1 O ARG B 183 N LYS B 91 SHEET 11 AA113 VAL B 189 ARG B 197 -1 O VAL B 195 N LEU B 179 SHEET 12 AA113 TYR B 142 ILE B 147 -1 N ILE B 143 O THR B 196 SHEET 13 AA113 HIS B 135 THR B 136 -1 N HIS B 135 O ILE B 144 SHEET 1 AA2 5 THR A 232 LYS A 234 0 SHEET 2 AA2 5 ARG A 208 LEU A 212 1 N ASP A 211 O LEU A 233 SHEET 3 AA2 5 SER A 275 ASP A 282 -1 O VAL A 278 N TYR A 210 SHEET 4 AA2 5 GLU A 351 ILE A 358 -1 O VAL A 352 N HIS A 281 SHEET 5 AA2 5 GLY A 340 LYS A 342 -1 N ILE A 341 O TYR A 353 SHEET 1 AA3 2 LEU A 271 MET A 272 0 SHEET 2 AA3 2 THR A 362 HIS A 363 -1 O THR A 362 N MET A 272 SHEET 1 AA4 5 THR B 232 LEU B 233 0 SHEET 2 AA4 5 ARG B 208 LEU B 212 1 N LYS B 209 O LEU B 233 SHEET 3 AA4 5 SER B 275 ASP B 282 -1 O LEU B 276 N LEU B 212 SHEET 4 AA4 5 GLU B 351 ILE B 358 -1 O ALA B 356 N LEU B 277 SHEET 5 AA4 5 GLY B 340 LYS B 342 -1 N ILE B 341 O TYR B 353 SHEET 1 AA5 2 LEU B 271 MET B 272 0 SHEET 2 AA5 2 THR B 362 HIS B 363 -1 O THR B 362 N MET B 272 LINK C ILE A 358 N PHD A 359 1555 1555 1.33 LINK C PHD A 359 N AILE A 360 1555 1555 1.33 LINK C PHD A 359 N BILE A 360 1555 1555 1.34 LINK C ILE B 358 N PHD B 359 1555 1555 1.34 LINK C PHD B 359 N ILE B 360 1555 1555 1.35 SITE 1 AC1 4 PHD A 359 THR A 362 OZ5 A 502 HOH A 645 SITE 1 AC2 16 PHE A 134 ILE A 143 LYS A 145 ILE A 147 SITE 2 AC2 16 ASP A 151 PHE A 178 ILE A 194 ASN A 198 SITE 3 AC2 16 VAL A 199 LYS A 209 THR A 232 LEU A 277 SITE 4 AC2 16 ILE A 358 PO4 A 501 HOH A 635 HOH A 652 SITE 1 AC3 3 ASP B 151 PHD B 359 OZ5 B 502 SITE 1 AC4 14 PHE B 134 ILE B 143 LYS B 145 ILE B 147 SITE 2 AC4 14 MET B 155 ILE B 194 ASN B 198 VAL B 199 SITE 3 AC4 14 LYS B 209 THR B 232 LEU B 277 ILE B 358 SITE 4 AC4 14 PO4 B 501 HOH B 615 CRYST1 43.900 99.388 104.302 90.00 93.65 90.00 P 1 21 1 4 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 0.022779 0.000000 0.001453 0.00000 SCALE2 0.000000 0.010062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009607 0.00000