HEADER NUCLEAR PROTEIN 02-MAY-21 7OE8 TITLE C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6R)-3- TITLE 2 OXABICYCLO[3.1.0]HEXAN-6-YL)-3-(1H-INDOL-4-YL)-N7-METHYL-2,3- TITLE 3 DIHYDROBENZOFURAN-5,7-DICARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, BROMODOMAIN, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CHUNG REVDAT 3 01-MAY-24 7OE8 1 REMARK REVDAT 2 25-AUG-21 7OE8 1 JRNL REVDAT 1 28-JUL-21 7OE8 0 JRNL AUTH S.C.C.LUCAS,S.J.ATKINSON,C.W.CHUNG,R.DAVIS,L.GORDON, JRNL AUTH 2 P.GRANDI,J.J.R.GRAY,T.GRIMES,A.PHILLIPOU,A.G.PRESTON, JRNL AUTH 3 R.K.PRINJHA,I.RIOJA,S.TAYLOR,N.C.O.TOMKINSON,I.WALL, JRNL AUTH 4 R.J.WATSON,J.WOOLVEN,E.H.DEMONT JRNL TITL OPTIMIZATION OF A SERIES OF 2,3-DIHYDROBENZOFURANS AS HIGHLY JRNL TITL 2 POTENT, SECOND BROMODOMAIN (BD2)-SELECTIVE, BROMO AND JRNL TITL 3 EXTRA-TERMINAL DOMAIN (BET) INHIBITORS. JRNL REF J.MED.CHEM. V. 64 10711 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34260229 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00344 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 (6-FEB-2020) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 29329 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1408 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.31 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.82 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE : 0.2212 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20 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 : 923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.12990 REMARK 3 B22 (A**2) : 1.23410 REMARK 3 B33 (A**2) : -3.36400 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) : 0.180 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.063 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.060 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.057 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.056 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 : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1009 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1362 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 361 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 168 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1009 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 116 ; 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 : 1018 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.85 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.35 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.70 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 7OE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-16 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 : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 15.80 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: IN HOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 300, 0.1M MES BUFFER PH6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K 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 35.96700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.19450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.96700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.19450 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 TOTAL BURIED SURFACE AREA: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 746 LIES ON A SPECIAL POSITION. 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 341 REMARK 465 SER A 342 REMARK 465 MET A 343 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 708 O HOH A 716 2.14 REMARK 500 O HOH A 628 O HOH A 685 2.16 REMARK 500 O HOH A 729 O HOH A 758 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 764 DISTANCE = 5.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V9Q A 503 DBREF 7OE8 A 344 455 UNP P25440 BRD2_HUMAN 344 455 SEQADV 7OE8 GLY A 341 UNP P25440 EXPRESSION TAG SEQADV 7OE8 SER A 342 UNP P25440 EXPRESSION TAG SEQADV 7OE8 MET A 343 UNP P25440 EXPRESSION TAG SEQRES 1 A 115 GLY SER MET GLY LYS LEU SER GLU GLN LEU LYS HIS CYS SEQRES 2 A 115 ASN GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA SEQRES 3 A 115 ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER SEQRES 4 A 115 ALA LEU GLY LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS SEQRES 5 A 115 PRO MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN SEQRES 6 A 115 ARG ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL SEQRES 7 A 115 ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO SEQRES 8 A 115 ASP HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP SEQRES 9 A 115 VAL PHE GLU PHE ARG TYR ALA LYS MET PRO ASP HET EDO A 501 4 HET EDO A 502 4 HET V9Q A 503 31 HETNAM EDO 1,2-ETHANEDIOL HETNAM V9Q (3S)-3-(1H-INDOL-4-YL)-N7-METHYL-N5-[(1R,5S)-3- HETNAM 2 V9Q OXABICYCLO[3.1.0]HEXAN-6-YL]-2,3-DIHYDRO-1-BENZOFURAN- HETNAM 3 V9Q 5,7-DICARBOXAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN V9Q N5-((1R,5S,6R)-3-OXABICYCLO[3.1.0]HEXAN-6-YL)-3-(1H- HETSYN 2 V9Q INDOL-4-YL)-N7-METHYL-2,3-DIHYDROBENZOFURAN-5,7- HETSYN 3 V9Q DICARBOXAMIDE FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 V9Q C24 H23 N3 O4 FORMUL 5 HOH *164(H2 O) HELIX 1 AA1 GLY A 344 LEU A 361 1 18 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 ALA A 451 1 19 SITE 1 AC1 8 TYR A 368 LYS A 402 ASP A 407 GLU A 413 SITE 2 AC1 8 MET A 438 LYS A 441 HOH A 603 HOH A 620 SITE 1 AC2 4 TYR A 426 LYS A 427 ASN A 429 HOH A 609 SITE 1 AC3 12 LYS A 351 TRP A 370 PRO A 371 LEU A 383 SITE 2 AC3 12 TYR A 428 ASN A 429 PRO A 430 VAL A 435 SITE 3 AC3 12 HOH A 629 HOH A 650 HOH A 651 HOH A 671 CRYST1 71.934 52.389 31.998 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 0.013902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031252 0.00000