HEADER TRANSCRIPTION 31-MAY-18 6DL2 TITLE BRD4 BROMODOMAIN 1 IN COMPLEX WITH HYB157 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.L.MEAGHER,J.A.STUCKEY REVDAT 2 11-OCT-23 6DL2 1 REMARK REVDAT 1 17-APR-19 6DL2 0 JRNL AUTH C.QIN,Y.HU,B.ZHOU,E.FERNANDEZ-SALAS,C.Y.YANG,L.LIU, JRNL AUTH 2 D.MCEACHERN,S.PRZYBRANOWSKI,M.WANG,J.STUCKEY,J.MEAGHER, JRNL AUTH 3 L.BAI,Z.CHEN,M.LIN,J.YANG,D.N.ZIAZADEH,F.XU,J.HU,W.XIANG, JRNL AUTH 4 L.HUANG,S.LI,B.WEN,D.SUN,S.WANG JRNL TITL DISCOVERY OF QCA570 AS AN EXCEPTIONALLY POTENT AND JRNL TITL 2 EFFICACIOUS PROTEOLYSIS TARGETING CHIMERA (PROTAC) DEGRADER JRNL TITL 3 OF THE BROMODOMAIN AND EXTRA-TERMINAL (BET) PROTEINS CAPABLE JRNL TITL 4 OF INDUCING COMPLETE AND DURABLE TUMOR REGRESSION. JRNL REF J. MED. CHEM. V. 61 6685 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30019901 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00506 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 22368 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 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 : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2874 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1843 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2749 REMARK 3 BIN R VALUE (WORKING SET) : 0.1827 REMARK 3 BIN FREE R VALUE : 0.2209 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.35 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 125 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 : 1037 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.46730 REMARK 3 B22 (A**2) : 3.02950 REMARK 3 B33 (A**2) : 2.43780 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) : 0.190 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.083 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.079 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.077 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.074 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 : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1107 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1513 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 375 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 203 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1107 ; 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 : 144 ; 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 : 1471 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.22 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.46 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 11.5408 -3.0734 -9.0600 REMARK 3 T TENSOR REMARK 3 T11: -0.0398 T22: -0.0508 REMARK 3 T33: -0.0131 T12: -0.0057 REMARK 3 T13: 0.0366 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.7633 L22: 1.3874 REMARK 3 L33: 2.4936 L12: -0.4799 REMARK 3 L13: -0.4105 L23: 0.5992 REMARK 3 S TENSOR REMARK 3 S11: -0.1070 S12: -0.0073 S13: -0.0908 REMARK 3 S21: 0.0522 S22: -0.0491 S23: 0.1525 REMARK 3 S31: 0.2083 S32: -0.0566 S33: 0.1560 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-15 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 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 : 22421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.19100 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4LYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.2 M POTASSIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, SITTING DROP, 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 18.75600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.65300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.65300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.75600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.56500 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 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 ASN A 42 CG OD1 ND2 REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 ASN A 116 CG OD1 ND2 REMARK 470 ASN A 117 CG OD1 ND2 REMARK 470 GLN A 123 CG CD OE1 NE2 REMARK 470 GLN A 159 CG CD OE1 NE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 GLU A 168 CG CD OE1 OE2 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 ASN A 117 72.23 38.58 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 GUJ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 DBREF 6DL2 A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6DL2 SER A 41 UNP O60885 EXPRESSION TAG SEQADV 6DL2 ASN A 42 UNP O60885 EXPRESSION TAG SEQADV 6DL2 ALA A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 128 SER ASN ALA ASN PRO PRO PRO PRO GLU THR SER ASN PRO SEQRES 2 A 128 ASN LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU SEQRES 3 A 128 LEU ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE SEQRES 4 A 128 ALA TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU SEQRES 5 A 128 ASN LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET SEQRES 6 A 128 ASP MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR SEQRES 7 A 128 TYR TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR SEQRES 8 A 128 MET PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP SEQRES 9 A 128 ASP ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE SEQRES 10 A 128 LEU GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET GUJ A 201 22 HET EDO A 202 4 HETNAM GUJ 3-BENZYL-2,9-DIMETHYL-4H,6H-THIENO[2,3-E][1,2, HETNAM 2 GUJ 4]TRIAZOLO[3,4-C][1,4]OXAZEPINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GUJ C17 H17 N3 O S FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *147(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 SITE 1 AC1 8 TRP A 81 PHE A 83 LEU A 92 LYS A 99 SITE 2 AC1 8 ASN A 140 ILE A 146 MET A 149 HOH A 301 SITE 1 AC2 5 ILE A 100 ILE A 101 LYS A 102 THR A 103 SITE 2 AC2 5 ASN A 135 CRYST1 37.512 43.130 79.306 90.00 90.00 90.00 P 21 21 21 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 0.026658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012609 0.00000