HEADER SIGNALING PROTEIN/INHIBITOR 03-JAN-17 5UEW TITLE BRD2 BROMODOMAIN2 WITH A-1360579 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 347-454; COMPND 5 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; COMPND 6 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 SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.H.PARK REVDAT 3 06-MAR-24 5UEW 1 REMARK REVDAT 2 24-MAY-17 5UEW 1 JRNL REVDAT 1 10-MAY-17 5UEW 0 JRNL AUTH L.WANG,J.K.PRATT,T.SOLTWEDEL,G.S.SHEPPARD,S.D.FIDANZE,D.LIU, JRNL AUTH 2 L.A.HASVOLD,R.A.MANTEI,J.H.HOLMS,W.J.MCCLELLAN,M.D.WENDT, JRNL AUTH 3 C.WADA,R.FREY,T.M.HANSEN,R.HUBBARD,C.H.PARK,L.LI,T.J.MAGOC, JRNL AUTH 4 D.H.ALBERT,X.LIN,S.E.WARDER,P.KOVAR,X.HUANG,D.WILCOX,R.WANG, JRNL AUTH 5 G.RAJARAMAN,A.M.PETROS,C.W.HUTCHINS,S.C.PANCHAL,C.SUN, JRNL AUTH 6 S.W.ELMORE,Y.SHEN,W.M.KATI,K.F.MCDANIEL JRNL TITL FRAGMENT-BASED, STRUCTURE-ENABLED DISCOVERY OF NOVEL JRNL TITL 2 PYRIDONES AND PYRIDONE MACROCYCLES AS POTENT BROMODOMAIN AND JRNL TITL 3 EXTRA-TERMINAL DOMAIN (BET) FAMILY BROMODOMAIN INHIBITORS. JRNL REF J. MED. CHEM. V. 60 3828 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28368119 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00017 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 18586 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 964 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.020 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.94 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.45 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2585 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2100 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2432 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.92 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 153 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1828 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.98490 REMARK 3 B22 (A**2) : -4.22990 REMARK 3 B33 (A**2) : 0.24500 REMARK 3 B12 (A**2) : 0.37010 REMARK 3 B13 (A**2) : -0.10370 REMARK 3 B23 (A**2) : 4.95800 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.260 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.162 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.145 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.164 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.146 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 : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1980 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2698 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 672 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 44 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 306 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1980 ; 20.000 ; 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 : 224 ; 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 : 2336 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.61 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.43 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 5UEW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225607. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-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 : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 2.11.7 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER : 10 MM HEPES PH 7.5 REMARK 280 100 MM NACL 5 MM DTT CRYSTALLIZATION : 15 % (V/V) ETHANOL TRIS REMARK 280 PH 7.0, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 B 452 21.58 -79.88 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 87D A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 87D B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UEU RELATED DB: PDB REMARK 900 RELATED ID: 5UF0 RELATED DB: PDB REMARK 900 RELATED ID: 5UEZ RELATED DB: PDB REMARK 900 RELATED ID: 5UEY RELATED DB: PDB REMARK 900 RELATED ID: 5UEX RELATED DB: PDB REMARK 900 RELATED ID: 5UEV RELATED DB: PDB REMARK 900 RELATED ID: 5UEP RELATED DB: PDB REMARK 900 RELATED ID: 5UET RELATED DB: PDB REMARK 900 RELATED ID: 5UES RELATED DB: PDB REMARK 900 RELATED ID: 5UER RELATED DB: PDB REMARK 900 RELATED ID: 5UEQ RELATED DB: PDB REMARK 900 RELATED ID: 5UEO RELATED DB: PDB DBREF 5UEW A 347 454 UNP P25440 BRD2_HUMAN 347 454 DBREF 5UEW B 347 454 UNP P25440 BRD2_HUMAN 347 454 SEQADV 5UEW GLY A 344 UNP P25440 EXPRESSION TAG SEQADV 5UEW SER A 345 UNP P25440 EXPRESSION TAG SEQADV 5UEW HIS A 346 UNP P25440 EXPRESSION TAG SEQADV 5UEW GLY B 344 UNP P25440 EXPRESSION TAG SEQADV 5UEW SER B 345 UNP P25440 EXPRESSION TAG SEQADV 5UEW HIS B 346 UNP P25440 EXPRESSION TAG SEQRES 1 A 111 GLY SER HIS SER GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 A 111 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 A 111 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 A 111 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 A 111 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 A 111 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 A 111 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 A 111 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 A 111 PHE ARG TYR ALA LYS MET PRO SEQRES 1 B 111 GLY SER HIS SER GLU GLN LEU LYS HIS CYS ASN GLY ILE SEQRES 2 B 111 LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA SEQRES 3 B 111 TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY SEQRES 4 B 111 LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP SEQRES 5 B 111 LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR SEQRES 6 B 111 ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET SEQRES 7 B 111 PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP SEQRES 8 B 111 VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU SEQRES 9 B 111 PHE ARG TYR ALA LYS MET PRO HET 87D A 501 48 HET 87D B 501 48 HETNAM 87D N-[3-(4-METHOXY-1-METHYL-6-OXO-1,6-DIHYDROPYRIDIN-3- HETNAM 2 87D YL)-4-PHENOXYPHENYL]METHANESULFONAMIDE FORMUL 3 87D 2(C20 H20 N2 O5 S) FORMUL 5 HOH *137(H2 O) HELIX 1 AA1 SER A 345 LEU A 361 1 17 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 LYS A 452 1 20 HELIX 10 AB1 SER B 345 LEU B 361 1 17 HELIX 11 AB2 SER B 362 LYS B 364 5 3 HELIX 12 AB3 HIS B 365 TRP B 370 1 6 HELIX 13 AB4 PRO B 371 TYR B 373 5 3 HELIX 14 AB5 ASP B 377 GLY B 382 1 6 HELIX 15 AB6 ASP B 385 ILE B 390 1 6 HELIX 16 AB7 ASP B 395 ASN B 405 1 11 HELIX 17 AB8 ASP B 410 ASN B 429 1 20 HELIX 18 AB9 HIS B 433 LYS B 452 1 20 SITE 1 AC1 14 TRP A 370 PRO A 371 PHE A 372 LYS A 374 SITE 2 AC1 14 PRO A 375 VAL A 376 ASP A 377 LEU A 381 SITE 3 AC1 14 ASN A 429 HIS A 433 VAL A 435 HOH A 611 SITE 4 AC1 14 HOH A 625 HOH A 628 SITE 1 AC2 11 TRP B 370 PRO B 371 PHE B 372 LYS B 374 SITE 2 AC2 11 VAL B 376 ASP B 377 LEU B 381 ASN B 429 SITE 3 AC2 11 HIS B 433 VAL B 435 HOH B 602 CRYST1 35.996 41.601 45.756 67.40 66.90 74.85 P 1 2 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 0.027781 -0.007522 -0.009978 0.00000 SCALE2 0.000000 0.024903 -0.008334 0.00000 SCALE3 0.000000 0.000000 0.025055 0.00000