HEADER TRANSFERASE 12-AUG-14 4UWH TITLE DISCOVERY OF (2S)-8-((3R)-3-METHYLMORPHOLIN-4-YL)-1-(3-METHYL-2-OXO- TITLE 2 BUTYL)-2-(TRIFLUOROMETHYL)-3,4-DIHYDRO-2H-PYRIMIDO(1,2-A)PYRIMIDIN-6- TITLE 3 ONE: A NOVEL POTENT AND SELECTIVE INHIBITOR OF VPS34 FOR THE TITLE 4 TREATMENT OF SOLID TUMORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VPS34 HELICAL AND KINASE DOMAINS, RESIDUES 282-879; COMPND 5 SYNONYM: PI3-KINASE TYPE 3, PI3K TYPE 3, PTDINS-3-KINASE TYPE 3, PHO COMPND 6 SPHATIDYLINOSITOL 3-KINASE P100 SUBUNIT, PHOSPHOINOSITIDE-3-KINASE COMPND 7 CLASS 3, HVPS34, PHOSPHOINOSITIDE 3-KINASE; COMPND 8 EC: 2.7.1.137; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TRANSFERASE, LIPID KINASE, AUTOPHAGY INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR B.PASQUIER,Y.EL-AHMAD,B.FILOCHE-ROMME,C.DUREUIL,F.FASSY, AUTHOR 2 P.Y.ABECASSIS,M.MATHIEU,T.BERTRAND,T.BENARD,C.BARRIERE,S.ELBATTI, AUTHOR 3 J.P.LETALLEC,V.SONNEFRAUD,M.BROLLO,L.DELBARRE,V.LOYAU,F.PILORGE, AUTHOR 4 L.BERTIN,P.RICHEPIN,J.ARIGON,J.R.LABROSSE,J.CLEMENT,F.DURAND, AUTHOR 5 R.COMBET,P.PERRAUT,V.LEROY,F.GAY,D.LEFRANCOIS,F.BRETIN, AUTHOR 6 J.P.MARQUETTE,N.MICHOT,A.CARON,C.CASTELL,L.SCHIO,G.MCCORT, AUTHOR 7 H.GOULAOUIC,C.GARCIA-ECHEVERRIA,B.RONAN REVDAT 4 01-MAY-24 4UWH 1 REMARK LINK REVDAT 3 21-JAN-15 4UWH 1 JRNL REVDAT 2 14-JAN-15 4UWH 1 REMARK REVDAT 1 26-NOV-14 4UWH 0 JRNL AUTH B.PASQUIER,Y.EL-AHMAD,B.FILOCHE-ROMME,C.DUREUIL-SIZAIRE, JRNL AUTH 2 F.FASSY,P.ABECASSIS,M.MATHIEU,T.BERTRAND,T.BENARD, JRNL AUTH 3 C.BARRIERE,S.EL BATTI,J.LETALLEC,V.SONNEFRAUD,M.BROLLO, JRNL AUTH 4 L.DELBARRE,V.LOYAU,F.PILORGE,L.BERTIN,P.RICHEPIN,J.ARIGON, JRNL AUTH 5 J.LABROSSE,J.CLEMENT,F.DURAND,R.COMBET,P.PERRAUT,V.LEROY, JRNL AUTH 6 F.GAY,D.LEFRANCOIS,F.BRETIN,J.MARQUETTE,N.MICHOT,A.CARON, JRNL AUTH 7 C.CASTELL,L.SCHIO,G.MCCORT,H.GOULAOUIC,C.GARCIA-ECHEVERRIA, JRNL AUTH 8 B.P.RONAN JRNL TITL DISCOVERY OF JRNL TITL 2 (2S)-8-[(3R)-3-METHYLMORPHOLIN-4-YL]-1-(3-METHYL-2-OXO-BUTYL JRNL TITL 3 )-2-(TRIFLUOROMETHYL)-3,4-DIHYDRO-2H-PYRIMIDO[1, JRNL TITL 4 2-A]PYRIMIDIN-6-ONE: A NOVEL POTENT AND SELECTIVE INHIBITOR JRNL TITL 5 OF VPS34 FOR THE TREATMENT OF SOLID TUMORS. JRNL REF J.MED.CHEM. V. 58 376 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 25402320 JRNL DOI 10.1021/JM5013352 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.9.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 60255 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.780 REMARK 3 FREE R VALUE TEST SET COUNT : 4690 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.48 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4250 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2272 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3916 REMARK 3 BIN R VALUE (WORKING SET) : 0.2254 REMARK 3 BIN FREE R VALUE : 0.2483 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.86 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 334 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.05210 REMARK 3 B22 (A**2) : 0.86070 REMARK 3 B33 (A**2) : 7.19140 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.212 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.127 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.116 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.123 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.114 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4614 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6245 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1655 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 138 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 648 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4614 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 591 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5763 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.93 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.19 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.34 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1290061513. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) OR REMARK 200 SI(311) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 75.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: INTERNAL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA CITRATE 1M PH8.0, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 44.41250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.72800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.41250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.72800 REMARK 290 SMTRY3 4 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 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 279 REMARK 465 ALA A 280 REMARK 465 MET A 281 REMARK 465 SER A 282 REMARK 465 ASP A 283 REMARK 465 HIS A 284 REMARK 465 THR A 418 REMARK 465 LYS A 419 REMARK 465 LYS A 420 REMARK 465 ASP A 421 REMARK 465 SER A 422 REMARK 465 GLN A 423 REMARK 465 SER A 424 REMARK 465 SER A 425 REMARK 465 VAL A 426 REMARK 465 SER A 427 REMARK 465 GLU A 428 REMARK 465 ASN A 429 REMARK 465 VAL A 430 REMARK 465 SER A 431 REMARK 465 ASN A 432 REMARK 465 SER A 433 REMARK 465 GLY A 434 REMARK 465 SER A 452 REMARK 465 VAL A 453 REMARK 465 SER A 454 REMARK 465 SER A 455 REMARK 465 PRO A 456 REMARK 465 PRO A 457 REMARK 465 PRO A 458 REMARK 465 ALA A 459 REMARK 465 SER A 460 REMARK 465 LYS A 461 REMARK 465 THR A 462 REMARK 465 LYS A 463 REMARK 465 GLU A 464 REMARK 465 VAL A 465 REMARK 465 PRO A 466 REMARK 465 ASP A 467 REMARK 465 GLY A 468 REMARK 465 GLU A 469 REMARK 465 VAL A 874 REMARK 465 VAL A 875 REMARK 465 GLU A 876 REMARK 465 GLN A 877 REMARK 465 ILE A 878 REMARK 465 HIS A 879 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 O TYR A 321 OG1 THR A 324 2.17 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 GLU A 596 88.68 -150.04 REMARK 500 THR A 668 78.00 -119.52 REMARK 500 ASP A 761 79.29 53.93 REMARK 500 PHE A 762 53.19 -92.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1875 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 439 O REMARK 620 2 HIS A 857 O 90.8 REMARK 620 3 SER A 861 OG 85.6 81.1 REMARK 620 4 HOH A2117 O 73.9 150.6 73.0 REMARK 620 5 HOH A2119 O 93.1 101.8 176.9 103.9 REMARK 620 6 HOH A2128 O 151.9 117.2 96.6 80.0 83.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1874 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 667 O REMARK 620 2 HOH A2271 O 99.7 REMARK 620 3 HOH A2272 O 106.4 88.0 REMARK 620 4 HOH A2273 O 125.6 82.1 127.9 REMARK 620 5 HOH A2280 O 90.3 169.7 91.6 90.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1874 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1875 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JXM A 1876 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UWK RELATED DB: PDB REMARK 900 DISCOVERY OF (2S)-8-((3R)-3-METHYLMORPHOLIN-4-YL)-1 -(3-METHYL-2- REMARK 900 OXO-BUTYL)-2-(TRIFLUOROMETHYL)-3,4- DIHYDRO-2H-PYRIMIDO(1,2-A) REMARK 900 PYRIMIDIN-6-ONE: A NOVEL POTENT AND SELECTIVE INHIBITOR OF VPS34 REMARK 900 FOR THE TREATMENT OF SOLID TUMORS REMARK 900 RELATED ID: 4UWL RELATED DB: PDB REMARK 900 DISCOVERY OF (2S)-8-((3R)-3-METHYLMORPHOLIN-4-YL)-1 -(3-METHYL-2- REMARK 900 OXO-BUTYL)-2-(TRIFLUOROMETHYL)-3,4- DIHYDRO-2H-PYRIMIDO(1,2-A) REMARK 900 PYRIMIDIN-6-ONE: A NOVEL POTENT AND SELECTIVE INHIBITOR OF VPS34 REMARK 900 FOR THE TREATMENT OF SOLID TUMORS DBREF 4UWH A 282 879 UNP Q8NEB9 PK3C3_HUMAN 282 879 SEQADV 4UWH GLY A 279 UNP Q8NEB9 EXPRESSION TAG SEQADV 4UWH ALA A 280 UNP Q8NEB9 EXPRESSION TAG SEQADV 4UWH MET A 281 UNP Q8NEB9 EXPRESSION TAG SEQRES 1 A 601 GLY ALA MET SER ASP HIS ASP LEU LYS PRO ASN ALA ALA SEQRES 2 A 601 THR ARG ASP GLN LEU ASN ILE ILE VAL SER TYR PRO PRO SEQRES 3 A 601 THR LYS GLN LEU THR TYR GLU GLU GLN ASP LEU VAL TRP SEQRES 4 A 601 LYS PHE ARG TYR TYR LEU THR ASN GLN GLU LYS ALA LEU SEQRES 5 A 601 THR LYS PHE LEU LYS CYS VAL ASN TRP ASP LEU PRO GLN SEQRES 6 A 601 GLU ALA LYS GLN ALA LEU GLU LEU LEU GLY LYS TRP LYS SEQRES 7 A 601 PRO MET ASP VAL GLU ASP SER LEU GLU LEU LEU SER SER SEQRES 8 A 601 HIS TYR THR ASN PRO THR VAL ARG ARG TYR ALA VAL ALA SEQRES 9 A 601 ARG LEU ARG GLN ALA ASP ASP GLU ASP LEU LEU MET TYR SEQRES 10 A 601 LEU LEU GLN LEU VAL GLN ALA LEU LYS TYR GLU ASN PHE SEQRES 11 A 601 ASP ASP ILE LYS ASN GLY LEU GLU PRO THR LYS LYS ASP SEQRES 12 A 601 SER GLN SER SER VAL SER GLU ASN VAL SER ASN SER GLY SEQRES 13 A 601 ILE ASN SER ALA GLU ILE ASP SER SER GLN ILE ILE THR SEQRES 14 A 601 SER PRO LEU PRO SER VAL SER SER PRO PRO PRO ALA SER SEQRES 15 A 601 LYS THR LYS GLU VAL PRO ASP GLY GLU ASN LEU GLU GLN SEQRES 16 A 601 ASP LEU CYS THR PHE LEU ILE SER ARG ALA CYS LYS ASN SEQRES 17 A 601 SER THR LEU ALA ASN TYR LEU TYR TRP TYR VAL ILE VAL SEQRES 18 A 601 GLU CYS GLU ASP GLN ASP THR GLN GLN ARG ASP PRO LYS SEQRES 19 A 601 THR HIS GLU MET TYR LEU ASN VAL MET ARG ARG PHE SER SEQRES 20 A 601 GLN ALA LEU LEU LYS GLY ASP LYS SER VAL ARG VAL MET SEQRES 21 A 601 ARG SER LEU LEU ALA ALA GLN GLN THR PHE VAL ASP ARG SEQRES 22 A 601 LEU VAL HIS LEU MET LYS ALA VAL GLN ARG GLU SER GLY SEQRES 23 A 601 ASN ARG LYS LYS LYS ASN GLU ARG LEU GLN ALA LEU LEU SEQRES 24 A 601 GLY ASP ASN GLU LYS MET ASN LEU SER ASP VAL GLU LEU SEQRES 25 A 601 ILE PRO LEU PRO LEU GLU PRO GLN VAL LYS ILE ARG GLY SEQRES 26 A 601 ILE ILE PRO GLU THR ALA THR LEU PHE LYS SER ALA LEU SEQRES 27 A 601 MET PRO ALA GLN LEU PHE PHE LYS THR GLU ASP GLY GLY SEQRES 28 A 601 LYS TYR PRO VAL ILE PHE LYS HIS GLY ASP ASP LEU ARG SEQRES 29 A 601 GLN ASP GLN LEU ILE LEU GLN ILE ILE SER LEU MET ASP SEQRES 30 A 601 LYS LEU LEU ARG LYS GLU ASN LEU ASP LEU LYS LEU THR SEQRES 31 A 601 PRO TYR LYS VAL LEU ALA THR SER THR LYS HIS GLY PHE SEQRES 32 A 601 MET GLN PHE ILE GLN SER VAL PRO VAL ALA GLU VAL LEU SEQRES 33 A 601 ASP THR GLU GLY SER ILE GLN ASN PHE PHE ARG LYS TYR SEQRES 34 A 601 ALA PRO SER GLU ASN GLY PRO ASN GLY ILE SER ALA GLU SEQRES 35 A 601 VAL MET ASP THR TYR VAL LYS SER CYS ALA GLY TYR CYS SEQRES 36 A 601 VAL ILE THR TYR ILE LEU GLY VAL GLY ASP ARG HIS LEU SEQRES 37 A 601 ASP ASN LEU LEU LEU THR LYS THR GLY LYS LEU PHE HIS SEQRES 38 A 601 ILE ASP PHE GLY TYR ILE LEU GLY ARG ASP PRO LYS PRO SEQRES 39 A 601 LEU PRO PRO PRO MET LYS LEU ASN LYS GLU MET VAL GLU SEQRES 40 A 601 GLY MET GLY GLY THR GLN SER GLU GLN TYR GLN GLU PHE SEQRES 41 A 601 ARG LYS GLN CYS TYR THR ALA PHE LEU HIS LEU ARG ARG SEQRES 42 A 601 TYR SER ASN LEU ILE LEU ASN LEU PHE SER LEU MET VAL SEQRES 43 A 601 ASP ALA ASN ILE PRO ASP ILE ALA LEU GLU PRO ASP LYS SEQRES 44 A 601 THR VAL LYS LYS VAL GLN ASP LYS PHE ARG LEU ASP LEU SEQRES 45 A 601 SER ASP GLU GLU ALA VAL HIS TYR MET GLN SER LEU ILE SEQRES 46 A 601 ASP GLU SER VAL HIS ALA LEU PHE ALA ALA VAL VAL GLU SEQRES 47 A 601 GLN ILE HIS HET NA A1874 1 HET NA A1875 1 HET JXM A1876 30 HETNAM NA SODIUM ION HETNAM JXM (8S)-9-[(2R)-2-HYDROXY-2-PHENYLETHYL]-2-(MORPHOLIN-4- HETNAM 2 JXM YL)-8-(TRIFLUOROMETHYL)-6,7,8,9-TETRAHYDRO-4H- HETNAM 3 JXM PYRIMIDO[1,2-A]PYRIMIDIN-4-ONE FORMUL 2 NA 2(NA 1+) FORMUL 4 JXM C20 H23 F3 N4 O3 FORMUL 5 HOH *381(H2 O) HELIX 1 1 ASN A 289 SER A 301 1 13 HELIX 2 2 THR A 309 PHE A 319 1 11 HELIX 3 3 PHE A 319 THR A 324 1 6 HELIX 4 4 ASN A 325 LYS A 328 5 4 HELIX 5 5 ALA A 329 LYS A 335 1 7 HELIX 6 6 LEU A 341 GLY A 353 1 13 HELIX 7 7 ASP A 359 LEU A 366 1 8 HELIX 8 8 ASN A 373 ARG A 385 1 13 HELIX 9 9 ASP A 388 LEU A 403 1 16 HELIX 10 10 LYS A 404 GLU A 406 5 3 HELIX 11 11 ASN A 407 GLY A 414 1 8 HELIX 12 12 ASN A 436 ILE A 440 5 5 HELIX 13 13 ASP A 441 ILE A 445 5 5 HELIX 14 14 ASP A 474 ASN A 486 1 13 HELIX 15 15 ASN A 486 ASP A 503 1 18 HELIX 16 16 ASP A 503 ASP A 510 1 8 HELIX 17 17 ASP A 510 LYS A 530 1 21 HELIX 18 18 ASP A 532 GLU A 562 1 31 HELIX 19 19 ASN A 565 ASP A 579 1 15 HELIX 20 20 ASP A 579 ASN A 584 1 6 HELIX 21 21 PRO A 606 ALA A 609 5 4 HELIX 22 22 LEU A 641 GLU A 661 1 21 HELIX 23 23 VAL A 690 GLY A 698 1 9 HELIX 24 24 SER A 699 ALA A 708 1 10 HELIX 25 25 GLY A 713 GLY A 716 5 4 HELIX 26 26 SER A 718 LEU A 739 1 22 HELIX 27 27 ASN A 780 GLY A 788 1 9 HELIX 28 28 SER A 792 TYR A 812 1 21 HELIX 29 29 TYR A 812 LEU A 822 1 11 HELIX 30 30 ILE A 828 LEU A 833 1 6 HELIX 31 31 GLU A 834 ASP A 836 5 3 HELIX 32 32 LYS A 837 PHE A 846 1 10 HELIX 33 33 SER A 851 ALA A 873 1 23 SHEET 1 AA 6 ILE A 591 LEU A 593 0 SHEET 2 AA 6 GLU A 596 ILE A 604 -1 N GLU A 596 O LEU A 593 SHEET 3 AA 6 ALA A 619 THR A 625 -1 O LYS A 624 N ARG A 602 SHEET 4 AA 6 LYS A 630 HIS A 637 -1 O TYR A 631 N PHE A 623 SHEET 5 AA 6 HIS A 679 GLN A 683 -1 O GLY A 680 N LYS A 636 SHEET 6 AA 6 VAL A 672 ALA A 674 -1 O LEU A 673 N PHE A 681 SHEET 1 AB 4 ILE A 591 LEU A 593 0 SHEET 2 AB 4 GLU A 596 ILE A 604 -1 N GLU A 596 O LEU A 593 SHEET 3 AB 4 ALA A 619 THR A 625 -1 O LYS A 624 N ARG A 602 SHEET 4 AB 4 THR A 610 LEU A 611 1 O THR A 610 N GLN A 620 SHEET 1 AC 3 VAL A 688 PRO A 689 0 SHEET 2 AC 3 LEU A 749 LEU A 751 -1 O LEU A 751 N VAL A 688 SHEET 3 AC 3 LEU A 757 HIS A 759 -1 O PHE A 758 N LEU A 750 LINK O GLU A 439 NA NA A1875 1555 1555 2.25 LINK O LEU A 667 NA NA A1874 1555 1555 2.30 LINK O HIS A 857 NA NA A1875 1554 1555 2.46 LINK OG SER A 861 NA NA A1875 1554 1555 2.30 LINK NA NA A1874 O HOH A2271 1555 1555 2.57 LINK NA NA A1874 O HOH A2272 1555 1555 2.37 LINK NA NA A1874 O HOH A2273 1555 1555 2.24 LINK NA NA A1874 O HOH A2280 1555 1555 2.48 LINK NA NA A1875 O HOH A2117 1555 1555 2.92 LINK NA NA A1875 O HOH A2119 1555 1555 2.32 LINK NA NA A1875 O HOH A2128 1555 1555 2.30 SITE 1 AC1 6 ARG A 659 LEU A 667 HOH A2271 HOH A2272 SITE 2 AC1 6 HOH A2273 HOH A2280 SITE 1 AC2 6 GLU A 439 HIS A 857 SER A 861 HOH A2117 SITE 2 AC2 6 HOH A2119 HOH A2128 SITE 1 AC3 16 PHE A 612 PRO A 618 ILE A 634 LYS A 636 SITE 2 AC3 16 TYR A 670 MET A 682 GLN A 683 PHE A 684 SITE 3 AC3 16 ILE A 685 SER A 687 LEU A 750 ILE A 760 SITE 4 AC3 16 ASP A 761 HOH A2248 HOH A2260 HOH A2320 CRYST1 88.825 145.456 61.352 90.00 90.00 90.00 P 21 21 2 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 0.011258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016299 0.00000