HEADER HYDROLASE 19-NOV-25 9XRJ TITLE CRYSTAL STRUCTURE OF MTH1 IN COMPLEX WITH ACORAMIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXIDIZED PURINE NUCLEOSIDE TRIPHOSPHATE HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,7,8-DIHYDRO-8-OXOGUANINE COMPND 5 TRIPHOSPHATASE,8-OXO-DGTPASE,METHYLATED PURINE NUCLEOSIDE COMPND 6 TRIPHOSPHATE HYDROLASE,NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF COMPND 7 1,NUDIX MOTIF 1; COMPND 8 EC: 3.6.1.56,3.6.1.-; 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 GENE: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, DRUG REPOSITIONING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.YOKOYAMA,T.NAKAMURA,M.GOTO,K.KUSAKA REVDAT 1 01-APR-26 9XRJ 0 JRNL AUTH T.YOKOYAMA,T.NAKAMURA,M.GOTO,K.KUSAKA JRNL TITL IDENTIFICATION OF ACORAMIDIS AS A REPURPOSED INHIBITOR OF JRNL TITL 2 THE DNA SANITIZATION ENZYME MUTT HOMOLOGUE 1. JRNL REF ACS PHARMACOL TRANSL SCI V. 9 698 2026 JRNL REFN ESSN 2575-910 JRNL PMID 41852632 JRNL DOI 10.1021/ACSPTSCI.5C00782 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21_5207: ???) 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1184 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 43.3900 - 3.7200 1.00 2982 158 0.1575 0.1830 REMARK 3 2 3.7200 - 2.9500 1.00 2841 149 0.1671 0.2219 REMARK 3 3 2.9500 - 2.5800 1.00 2811 148 0.1979 0.2508 REMARK 3 4 2.5800 - 2.3400 1.00 2795 147 0.1983 0.2713 REMARK 3 5 2.3400 - 2.1800 1.00 2786 147 0.1873 0.2586 REMARK 3 6 2.1800 - 2.0500 1.00 2770 146 0.1949 0.2525 REMARK 3 7 2.0500 - 1.9400 1.00 2751 144 0.2119 0.3008 REMARK 3 8 1.9400 - 1.8600 1.00 2754 145 0.2315 0.3118 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 2671 REMARK 3 ANGLE : 0.907 3611 REMARK 3 CHIRALITY : 0.084 369 REMARK 3 PLANARITY : 0.008 470 REMARK 3 DIHEDRAL : 17.166 1001 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 9XRJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1300066067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-25 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23680 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 44.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M SODIUM CITRATE, 0.2M SODIUM REMARK 280 CHLORIDE, 0.1M CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.16000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.16000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.73000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 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 HOH A 377 O HOH A 399 1.99 REMARK 500 NE2 GLN B 16 O HOH B 301 2.09 REMARK 500 OE1 GLU B 41 O HOH B 302 2.15 REMARK 500 OG1 THR B 60 O HOH B 303 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 9XRJ A 1 156 UNP P36639 8ODP_HUMAN 1 156 DBREF 9XRJ B 1 156 UNP P36639 8ODP_HUMAN 1 156 SEQADV 9XRJ LYS A 2 UNP P36639 GLY 2 CONFLICT SEQADV 9XRJ SER A 104 UNP P36639 CYS 104 CONFLICT SEQADV 9XRJ LYS B 2 UNP P36639 GLY 2 CONFLICT SEQADV 9XRJ SER B 104 UNP P36639 CYS 104 CONFLICT SEQRES 1 A 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL SEQRES 1 B 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 B 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 B 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 B 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 B 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 B 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 B 156 GLU LEU MET ASP VAL HIS VAL PHE CYS THR ASP SER ILE SEQRES 8 B 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 B 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 B 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 B 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 B 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HET 16V A 201 21 HET 16V B 201 21 HETNAM 16V 3-[3-(3,5-DIMETHYL-1H-PYRAZOL-4-YL)PROPOXY]-4- HETNAM 2 16V FLUOROBENZOIC ACID FORMUL 3 16V 2(C15 H17 F N2 O3) FORMUL 5 HOH *248(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 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 THR A 8 O GLY A 37 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 GLN A 92 0 SHEET 5 AA2 7 THR A 60 PHE A 74 -1 N ILE A 70 O VAL A 83 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 THR A 144 N GLN A 140 SHEET 1 AA3 4 TRP B 32 ASN B 33 0 SHEET 2 AA3 4 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA3 4 SER B 4 GLN B 14 -1 N GLN B 14 O ARG B 17 SHEET 4 AA3 4 MET B 101 PHE B 106 0 SHEET 1 AA4 7 PHE B 35 LYS B 38 0 SHEET 2 AA4 7 SER B 4 GLN B 14 -1 N VAL B 10 O PHE B 35 SHEET 3 AA4 7 ARG B 17 LYS B 23 -1 O ARG B 17 N GLN B 14 SHEET 4 AA4 7 LEU B 80 GLN B 92 0 SHEET 5 AA4 7 THR B 60 PHE B 74 -1 N ALA B 63 O ASP B 89 SHEET 6 AA4 7 PHE B 133 GLN B 140 1 O PHE B 139 N GLU B 73 SHEET 7 AA4 7 THR B 144 GLU B 152 -1 O ASP B 147 N LYS B 138 CRYST1 46.320 47.460 123.860 90.00 90.00 90.00 P 21 21 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 0.021589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008074 0.00000 CONECT 2563 2564 CONECT 2564 2563 2565 2566 CONECT 2565 2564 CONECT 2566 2564 2567 2568 CONECT 2567 2566 2572 CONECT 2568 2566 2569 CONECT 2569 2568 2570 CONECT 2570 2569 2571 2572 CONECT 2571 2570 CONECT 2572 2567 2570 2573 CONECT 2573 2572 2574 CONECT 2574 2573 2575 CONECT 2575 2574 2576 CONECT 2576 2575 2577 CONECT 2577 2576 2578 2582 CONECT 2578 2577 2579 2580 CONECT 2579 2578 CONECT 2580 2578 2581 CONECT 2581 2580 2582 CONECT 2582 2577 2581 2583 CONECT 2583 2582 CONECT 2584 2585 CONECT 2585 2584 2586 2587 CONECT 2586 2585 CONECT 2587 2585 2588 2589 CONECT 2588 2587 2593 CONECT 2589 2587 2590 CONECT 2590 2589 2591 CONECT 2591 2590 2592 2593 CONECT 2592 2591 CONECT 2593 2588 2591 2594 CONECT 2594 2593 2595 CONECT 2595 2594 2596 CONECT 2596 2595 2597 CONECT 2597 2596 2598 CONECT 2598 2597 2599 2603 CONECT 2599 2598 2600 2601 CONECT 2600 2599 CONECT 2601 2599 2602 CONECT 2602 2601 2603 CONECT 2603 2598 2602 2604 CONECT 2604 2603 MASTER 222 0 2 8 22 0 0 6 2826 2 42 24 END