HEADER HYDROLASE/HYDROLASE INHIBITOR 24-OCT-19 6US2 TITLE MTH1 IN COMPLEX WITH COMPOUND 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE,NUCLEOSIDE COMPND 5 DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 6 EC: 3.6.1.55,3.6.1.56; 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: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, NUDT1, NUDIX HYDROLASE, INHIBITOR, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.E.R.NEWBY,E.B.LANSDON REVDAT 2 11-OCT-23 6US2 1 REMARK REVDAT 1 01-APR-20 6US2 0 JRNL AUTH J.FARAND,J.E.KROPF,P.BLOMGREN,J.XU,A.C.SCHMITT,Z.E.NEWBY, JRNL AUTH 2 T.WANG,E.MURAKAMI,O.BARAUSKAS,J.SUDHAMSU,J.Y.FENG, JRNL AUTH 3 A.NIEDZIELA-MAJKA,B.E.SCHULTZ,K.SCHWARTZ, JRNL AUTH 4 S.VIATCHENKO-KARPINSKI,D.KORNYEYEV,A.KASHISHIAN,P.FAN, JRNL AUTH 5 X.CHEN,E.B.LANSDON,M.O.PORTS,K.S.CURRIE,W.J.WATKINS, JRNL AUTH 6 G.T.NOTTE JRNL TITL DISCOVERY OF POTENT AND SELECTIVE MTH1 INHIBITORS FOR JRNL TITL 2 ONCOLOGY: ENABLING RAPID TARGET (IN)VALIDATION. JRNL REF ACS MED.CHEM.LETT. V. 11 358 2020 JRNL REFN ISSN 1948-5875 JRNL PMID 32184970 JRNL DOI 10.1021/ACSMEDCHEMLETT.9B00420 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.227 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 13275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.004 REMARK 3 FREE R VALUE TEST SET COUNT : 1328 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 31.8911 - 3.7426 0.98 1482 166 0.1656 0.2151 REMARK 3 2 3.7426 - 2.9713 0.99 1419 157 0.1732 0.2126 REMARK 3 3 2.9713 - 2.5959 0.97 1348 150 0.1974 0.2698 REMARK 3 4 2.5959 - 2.3587 0.96 1342 149 0.1855 0.2422 REMARK 3 5 2.3587 - 2.1896 0.95 1323 147 0.1654 0.2218 REMARK 3 6 2.1896 - 2.0606 0.95 1312 145 0.1715 0.2362 REMARK 3 7 2.0606 - 1.9574 0.93 1287 143 0.1759 0.2852 REMARK 3 8 1.9574 - 1.8722 0.91 1253 140 0.1786 0.2637 REMARK 3 9 1.8722 - 1.8001 0.87 1181 131 0.2015 0.2376 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.175 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.926 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.34 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 : 0.008 1340 REMARK 3 ANGLE : 1.181 1820 REMARK 3 CHIRALITY : 0.053 187 REMARK 3 PLANARITY : 0.006 236 REMARK 3 DIHEDRAL : 13.243 502 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 6US2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000245088. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14073 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 : 3.700 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: 3ZR0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 6000, 0.1M SODIUM ACETATE PH REMARK 280 4.0, 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.97650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.33600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.97650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.33600 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY 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 62 -73.94 -94.60 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 S3O A 201 DBREF 6US2 A 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 6US2 GLY A -2 UNP P36639 EXPRESSION TAG SEQADV 6US2 SER A -1 UNP P36639 EXPRESSION TAG SEQADV 6US2 HIS A 0 UNP P36639 EXPRESSION TAG SEQRES 1 A 159 GLY SER HIS MET GLY ALA SER ARG LEU TYR THR LEU VAL SEQRES 2 A 159 LEU VAL LEU GLN PRO GLN ARG VAL LEU LEU GLY MET LYS SEQRES 3 A 159 LYS ARG GLY PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY SEQRES 4 A 159 GLY LYS VAL GLN GLU GLY GLU THR ILE GLU ASP GLY ALA SEQRES 5 A 159 ARG ARG GLU LEU GLN GLU GLU SER GLY LEU THR VAL ASP SEQRES 6 A 159 ALA LEU HIS LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL SEQRES 7 A 159 GLY GLU PRO GLU LEU MET ASP VAL HIS VAL PHE CYS THR SEQRES 8 A 159 ASP SER ILE GLN GLY THR PRO VAL GLU SER ASP GLU MET SEQRES 9 A 159 ARG PRO CYS TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS SEQRES 10 A 159 ASP MET TRP PRO ASP ASP SER TYR TRP PHE PRO LEU LEU SEQRES 11 A 159 LEU GLN LYS LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN SEQRES 12 A 159 GLY GLN ASP THR ILE LEU ASP TYR THR LEU ARG GLU VAL SEQRES 13 A 159 ASP THR VAL HET S3O A 201 22 HETNAM S3O N-[5-(2,3-DIMETHYLPHENYL)-1,2,3,4-TETRAHYDRO-1,6- HETNAM 2 S3O NAPHTHYRIDIN-7-YL]ACETAMIDE FORMUL 2 S3O C18 H21 N3 O FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 ASP A 109 ILE A 111 5 3 HELIX 3 AA3 PRO A 112 MET A 116 5 5 HELIX 4 AA4 TRP A 117 PRO A 118 5 2 HELIX 5 AA5 ASP A 119 GLN A 129 1 11 SHEET 1 AA1 4 TRP A 32 ASN A 33 0 SHEET 2 AA1 4 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 4 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA1 4 MET A 101 GLN A 107 0 SHEET 1 AA2 7 PHE A 35 LYS A 38 0 SHEET 2 AA2 7 SER A 4 LEU A 13 -1 N VAL A 10 O PHE A 35 SHEET 3 AA2 7 ARG A 17 LYS A 23 -1 O LEU A 19 N VAL A 12 SHEET 4 AA2 7 LEU A 80 THR A 88 0 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N GLY A 68 O VAL A 85 SHEET 6 AA2 7 LYS A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 VAL A 153 -1 O ASP A 147 N LYS A 138 SHEET 1 AA3 2 THR A 60 VAL A 61 0 SHEET 2 AA3 2 ILE A 91 GLN A 92 -1 O GLN A 92 N THR A 60 SITE 1 AC1 13 TYR A 7 THR A 8 LEU A 9 PHE A 27 SITE 2 AC1 13 ASN A 33 GLY A 34 GLY A 37 PHE A 72 SITE 3 AC1 13 VAL A 83 TRP A 117 ASP A 119 ASP A 120 SITE 4 AC1 13 PHE A 124 CRYST1 36.315 59.953 66.672 90.00 90.00 90.00 P 2 21 21 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 0.027537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016680 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014999 0.00000