HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 11-MAR-22 7U9Y TITLE WDR5 BOUND TO 2-(3,5-DIMETHOXYBENZYL)-7-((2-METHYL-1H-IMIDAZOL-1-YL) TITLE 2 METHYL)-5-(1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL)-3,4- TITLE 3 DIHYDROISOQUINOLIN-1(2H)-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD REPEAT-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BMP2-INDUCED 3-KB GENE PROTEIN; COMPND 5 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: WDR5, BIG3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS TRANSCRIPTION-TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.RIETZ REVDAT 3 18-OCT-23 7U9Y 1 REMARK REVDAT 2 11-MAY-22 7U9Y 1 JRNL REVDAT 1 27-APR-22 7U9Y 0 JRNL AUTH K.B.TEUSCHER,K.M.MEYERS,Q.WEI,J.J.MILLS,J.TIAN,J.ALVARADO, JRNL AUTH 2 J.SAI,M.VAN MEVEREN,T.M.SOUTH,T.A.RIETZ,B.ZHAO,W.J.MOORE, JRNL AUTH 3 G.M.STOTT,W.P.TANSEY,T.LEE,S.W.FESIK JRNL TITL DISCOVERY OF POTENT ORALLY BIOAVAILABLE WD REPEAT DOMAIN 5 JRNL TITL 2 (WDR5) INHIBITORS USING A PHARMACOPHORE-BASED OPTIMIZATION. JRNL REF J.MED.CHEM. V. 65 6287 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35436124 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00195 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1155 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 29.5500 - 3.8000 1.00 2960 127 0.1362 0.1712 REMARK 3 2 3.8000 - 3.0200 1.00 2819 144 0.1336 0.1499 REMARK 3 3 3.0200 - 2.6400 1.00 2766 146 0.1517 0.1754 REMARK 3 4 2.6400 - 2.4000 1.00 2751 124 0.1593 0.2342 REMARK 3 5 2.4000 - 2.2200 1.00 2738 155 0.1557 0.2090 REMARK 3 6 2.2200 - 2.0900 1.00 2724 140 0.1496 0.2037 REMARK 3 7 2.0900 - 1.9900 0.99 2669 178 0.1640 0.2366 REMARK 3 8 1.9900 - 1.9000 0.99 2694 141 0.1879 0.2401 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.07 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 7U9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-22 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23402 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 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: PHASER REMARK 200 STARTING MODEL: 3EG6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, AMMONIUM ACETATE, PEG 3350, REMARK 280 BENZAMIDINE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 40.62950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.06100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.62950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.06100 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 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 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 LYS A 109 7.59 80.44 REMARK 500 GLU A 151 2.97 80.44 REMARK 500 LEU A 234 38.29 -80.40 REMARK 500 ASN A 257 85.59 -150.14 REMARK 500 LYS A 259 -31.11 -132.37 REMARK 500 LEU A 321 -165.56 -79.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 7U9Y A 30 334 UNP P61964 WDR5_HUMAN 30 334 SEQRES 1 A 305 PRO VAL LYS PRO ASN TYR ALA LEU LYS PHE THR LEU ALA SEQRES 2 A 305 GLY HIS THR LYS ALA VAL SER SER VAL LYS PHE SER PRO SEQRES 3 A 305 ASN GLY GLU TRP LEU ALA SER SER SER ALA ASP LYS LEU SEQRES 4 A 305 ILE LYS ILE TRP GLY ALA TYR ASP GLY LYS PHE GLU LYS SEQRES 5 A 305 THR ILE SER GLY HIS LYS LEU GLY ILE SER ASP VAL ALA SEQRES 6 A 305 TRP SER SER ASP SER ASN LEU LEU VAL SER ALA SER ASP SEQRES 7 A 305 ASP LYS THR LEU LYS ILE TRP ASP VAL SER SER GLY LYS SEQRES 8 A 305 CYS LEU LYS THR LEU LYS GLY HIS SER ASN TYR VAL PHE SEQRES 9 A 305 CYS CYS ASN PHE ASN PRO GLN SER ASN LEU ILE VAL SER SEQRES 10 A 305 GLY SER PHE ASP GLU SER VAL ARG ILE TRP ASP VAL LYS SEQRES 11 A 305 THR GLY LYS CYS LEU LYS THR LEU PRO ALA HIS SER ASP SEQRES 12 A 305 PRO VAL SER ALA VAL HIS PHE ASN ARG ASP GLY SER LEU SEQRES 13 A 305 ILE VAL SER SER SER TYR ASP GLY LEU CYS ARG ILE TRP SEQRES 14 A 305 ASP THR ALA SER GLY GLN CYS LEU LYS THR LEU ILE ASP SEQRES 15 A 305 ASP ASP ASN PRO PRO VAL SER PHE VAL LYS PHE SER PRO SEQRES 16 A 305 ASN GLY LYS TYR ILE LEU ALA ALA THR LEU ASP ASN THR SEQRES 17 A 305 LEU LYS LEU TRP ASP TYR SER LYS GLY LYS CYS LEU LYS SEQRES 18 A 305 THR TYR THR GLY HIS LYS ASN GLU LYS TYR CYS ILE PHE SEQRES 19 A 305 ALA ASN PHE SER VAL THR GLY GLY LYS TRP ILE VAL SER SEQRES 20 A 305 GLY SER GLU ASP ASN LEU VAL TYR ILE TRP ASN LEU GLN SEQRES 21 A 305 THR LYS GLU ILE VAL GLN LYS LEU GLN GLY HIS THR ASP SEQRES 22 A 305 VAL VAL ILE SER THR ALA CYS HIS PRO THR GLU ASN ILE SEQRES 23 A 305 ILE ALA SER ALA ALA LEU GLU ASN ASP LYS THR ILE LYS SEQRES 24 A 305 LEU TRP LYS SER ASP CYS HET BEN A 401 9 HET M4U A 402 39 HETNAM BEN BENZAMIDINE HETNAM M4U (5P)-2-[(3,5-DIMETHOXYPHENYL)METHYL]-7-[(2-METHYL-1H- HETNAM 2 M4U IMIDAZOL-1-YL)METHYL]-5-[1-METHYL-3-(TRIFLUOROMETHYL)- HETNAM 3 M4U 1H-PYRAZOL-4-YL]-3,4-DIHYDROISOQUINOLIN-1(2H)-ONE FORMUL 2 BEN C7 H8 N2 FORMUL 3 M4U C28 H28 F3 N5 O3 FORMUL 4 HOH *304(H2 O) SHEET 1 AA1 4 ALA A 36 LEU A 41 0 SHEET 2 AA1 4 ILE A 327 LYS A 331 -1 O ILE A 327 N LEU A 41 SHEET 3 AA1 4 ILE A 315 ALA A 320 -1 N ILE A 316 O TRP A 330 SHEET 4 AA1 4 VAL A 304 CYS A 309 -1 N ALA A 308 O ALA A 317 SHEET 1 AA2 4 VAL A 48 PHE A 53 0 SHEET 2 AA2 4 TRP A 59 SER A 64 -1 O ALA A 61 N LYS A 52 SHEET 3 AA2 4 ILE A 69 GLY A 73 -1 O TRP A 72 N LEU A 60 SHEET 4 AA2 4 PHE A 79 ILE A 83 -1 O ILE A 83 N ILE A 69 SHEET 1 AA3 4 ILE A 90 TRP A 95 0 SHEET 2 AA3 4 LEU A 101 SER A 106 -1 O ALA A 105 N SER A 91 SHEET 3 AA3 4 LEU A 111 ASP A 115 -1 O TRP A 114 N LEU A 102 SHEET 4 AA3 4 CYS A 121 LEU A 125 -1 O LEU A 125 N LEU A 111 SHEET 1 AA4 4 VAL A 132 PHE A 137 0 SHEET 2 AA4 4 LEU A 143 SER A 148 -1 O VAL A 145 N ASN A 136 SHEET 3 AA4 4 VAL A 153 ASP A 157 -1 O TRP A 156 N ILE A 144 SHEET 4 AA4 4 CYS A 163 LEU A 167 -1 O LEU A 167 N VAL A 153 SHEET 1 AA5 4 VAL A 174 PHE A 179 0 SHEET 2 AA5 4 LEU A 185 SER A 190 -1 O VAL A 187 N HIS A 178 SHEET 3 AA5 4 CYS A 195 ASP A 199 -1 O TRP A 198 N ILE A 186 SHEET 4 AA5 4 CYS A 205 LEU A 209 -1 O LEU A 209 N CYS A 195 SHEET 1 AA6 4 VAL A 217 PHE A 222 0 SHEET 2 AA6 4 TYR A 228 THR A 233 -1 O ALA A 232 N PHE A 219 SHEET 3 AA6 4 THR A 237 ASP A 242 -1 O TRP A 241 N ILE A 229 SHEET 4 AA6 4 LYS A 247 TYR A 252 -1 O LYS A 247 N ASP A 242 SHEET 1 AA7 4 ALA A 264 SER A 267 0 SHEET 2 AA7 4 TRP A 273 SER A 276 -1 O VAL A 275 N ASN A 265 SHEET 3 AA7 4 VAL A 283 ASN A 287 -1 O TYR A 284 N SER A 276 SHEET 4 AA7 4 ILE A 293 LEU A 297 -1 O LEU A 297 N VAL A 283 CRYST1 81.259 86.122 41.094 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 0.012306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024334 0.00000