HEADER GENE REGULATION 14-JAN-21 7LEJ TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN BRDT BOUND TITLE 2 TO VOLASERTIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN TESTIS-SPECIFIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CANCER/TESTIS ANTIGEN 9,CT9,RING3-LIKE 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: BRDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BRDT, BET, PLK1, TESTIS SPECIFIC, BROMODOMAIN, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAN,M.R.KARIM,E.SCHONBRUNN REVDAT 4 18-OCT-23 7LEJ 1 REMARK REVDAT 3 24-NOV-21 7LEJ 1 JRNL REVDAT 2 17-NOV-21 7LEJ 1 JRNL REVDAT 1 14-JUL-21 7LEJ 0 JRNL AUTH R.M.KARIM,M.J.BIKOWITZ,A.CHAN,J.Y.ZHU,D.GRASSIE,A.BECKER, JRNL AUTH 2 N.BERNDT,S.GUNAWAN,N.J.LAWRENCE,E.SCHONBRUNN JRNL TITL DIFFERENTIAL BET BROMODOMAIN INHIBITION BY JRNL TITL 2 DIHYDROPTERIDINONE AND PYRIMIDODIAZEPINONE KINASE JRNL TITL 3 INHIBITORS. JRNL REF J.MED.CHEM. V. 64 15772 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34710325 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01096 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.080 REMARK 3 FREE R VALUE TEST SET COUNT : 998 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 36.4500 - 3.3088 1.00 2302 149 0.1725 0.1798 REMARK 3 2 3.3088 - 2.6265 1.00 2221 144 0.1982 0.2183 REMARK 3 3 2.6265 - 2.2946 1.00 2194 142 0.1991 0.2247 REMARK 3 4 2.2946 - 2.0848 1.00 2196 143 0.2032 0.2423 REMARK 3 5 2.0848 - 1.9354 1.00 2173 141 0.2158 0.2568 REMARK 3 6 1.9354 - 1.8213 1.00 2185 141 0.2056 0.2330 REMARK 3 7 1.8213 - 1.7301 0.99 2145 138 0.2074 0.2435 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.25 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.0678 -30.3345 6.4723 REMARK 3 T TENSOR REMARK 3 T11: 0.2566 T22: 0.2223 REMARK 3 T33: 0.1677 T12: -0.1190 REMARK 3 T13: -0.0213 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.7868 L22: 3.4404 REMARK 3 L33: 1.3238 L12: -0.3721 REMARK 3 L13: 0.1940 L23: -1.5070 REMARK 3 S TENSOR REMARK 3 S11: -0.1883 S12: 0.1130 S13: 0.0069 REMARK 3 S21: -0.5003 S22: 0.2287 S23: 0.0221 REMARK 3 S31: 0.1210 S32: -0.0429 S33: -0.0411 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 7LEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-19 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 : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 36.455 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.84 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.15 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.540 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: 5VBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M SODIUM CACODYLATE TRIHYDRATE (PH 6.5), 20 % W/V PEG 8,000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.54000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.77000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.77000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.54000 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 ILE A 378 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 ND1 HIS A 372 O HOH A 501 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 529 O HOH A 529 6555 2.16 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 LEU A 306 74.94 -104.00 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 IBI A 401 DBREF 7LEJ A 266 378 UNP Q58F21 BRDT_HUMAN 266 378 SEQADV 7LEJ ALA A 257 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ ALA A 258 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ TYR A 259 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ PHE A 260 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ GLN A 261 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ GLY A 262 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ ALA A 263 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ ALA A 264 UNP Q58F21 EXPRESSION TAG SEQADV 7LEJ SER A 265 UNP Q58F21 EXPRESSION TAG SEQRES 1 A 122 ALA ALA TYR PHE GLN GLY ALA ALA SER THR VAL LYS VAL SEQRES 2 A 122 THR GLU GLN LEU ARG HIS CYS SER GLU ILE LEU LYS GLU SEQRES 3 A 122 MET LEU ALA LYS LYS HIS PHE SER TYR ALA TRP PRO PHE SEQRES 4 A 122 TYR ASN PRO VAL ASP VAL ASN ALA LEU GLY LEU HIS ASN SEQRES 5 A 122 TYR TYR ASP VAL VAL LYS ASN PRO MET ASP LEU GLY THR SEQRES 6 A 122 ILE LYS GLU LYS MET ASP ASN GLN GLU TYR LYS ASP ALA SEQRES 7 A 122 TYR LYS PHE ALA ALA ASP VAL ARG LEU MET PHE MET ASN SEQRES 8 A 122 CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL VAL THR SEQRES 9 A 122 MET ALA ARG MET LEU GLN ASP VAL PHE GLU THR HIS PHE SEQRES 10 A 122 SER LYS ILE PRO ILE HET IBI A 401 45 HETNAM IBI N-{TRANS-4-[4-(CYCLOPROPYLMETHYL)PIPERAZIN-1- HETNAM 2 IBI YL]CYCLOHEXYL}-4-{[(7R)-7-ETHYL-5-METHYL-8-(1- HETNAM 3 IBI METHYLETHYL)-6-OXO-5,6,7,8-TETRAHYDROPTERIDIN-2- HETNAM 4 IBI YL]AMINO}-3-METHOXYBENZAMIDE HETSYN IBI VOLASERTIB FORMUL 2 IBI C34 H50 N8 O3 FORMUL 3 HOH *68(H2 O) HELIX 1 AA1 ALA A 257 ALA A 285 1 29 HELIX 2 AA2 HIS A 288 TRP A 293 1 6 HELIX 3 AA3 PRO A 294 TYR A 296 5 3 HELIX 4 AA4 ASP A 300 GLY A 305 1 6 HELIX 5 AA5 ASN A 308 VAL A 313 1 6 HELIX 6 AA6 ASP A 318 ASN A 328 1 11 HELIX 7 AA7 ASP A 333 ASN A 352 1 20 HELIX 8 AA8 HIS A 356 SER A 374 1 19 SITE 1 AC1 12 TYR A 259 ALA A 263 PRO A 294 VAL A 299 SITE 2 AC1 12 ALA A 303 LEU A 304 LEU A 306 TYR A 309 SITE 3 AC1 12 ASN A 352 HIS A 356 HOH A 508 HOH A 530 CRYST1 72.910 72.910 50.310 90.00 90.00 120.00 P 32 2 1 6 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 0.013716 0.007919 0.000000 0.00000 SCALE2 0.000000 0.015837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019877 0.00000