HEADER CELL CYCLE 02-APR-21 7MCE TITLE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX TITLE 2 WITH 2-{(7P)-7-(1,4-DIMETHYL-1H-1,2,3-TRIAZOL-5-YL)-8-FLUORO-5-[(S)- TITLE 3 (OXAN-4-YL)(PHENYL)METHYL]-5H-PYRIDO[3,2-B]INDOL-3-YL}PROPAN-2-OL 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS BROMODOMAIN-CONTAINING PROTEIN 4 ISOFORM LONG, BRD4, BROMODOMAIN KEYWDS 2 CONTAINING PROTEIN 4, CAP, HUNK1, MCAP, MITOTIC CHROMOSOME KEYWDS 3 ASSOCIATED PROTEIN SGC, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR S.SHERIFF REVDAT 3 18-OCT-23 7MCE 1 REMARK REVDAT 2 06-OCT-21 7MCE 1 JRNL REVDAT 1 29-SEP-21 7MCE 0 JRNL AUTH M.D.HILL,C.QUESNELLE,J.TOKARSKI,H.FANG,C.FANSLAU,Z.HAARHOFF, JRNL AUTH 2 M.KRAMER,S.MADARI,A.WIEBESIEK,J.MORRISON, JRNL AUTH 3 J.SIMMERMACHER-MAYER,M.SINZ,R.WESTHOUSE,C.XIE,J.ZHAO, JRNL AUTH 4 L.HUANG,S.SHERIFF,C.YAN,F.MARSILIO,G.EVERLOF,T.ZVYAGA,F.LEE, JRNL AUTH 5 A.V.GAVAI,A.P.DEGNAN JRNL TITL DEVELOPMENT OF BET INHIBITORS AS POTENTIAL TREATMENTS FOR JRNL TITL 2 CANCER: A NEW CARBOLINE CHEMOTYPE. JRNL REF BIOORG.MED.CHEM.LETT. V. 51 28376 2021 JRNL REFN ESSN 1464-3405 JRNL PMID 34560263 JRNL DOI 10.1016/J.BMCL.2021.128376 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13609 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.250 REMARK 3 FREE R VALUE TEST SET COUNT : 987 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 : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2715 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2973 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2491 REMARK 3 BIN R VALUE (WORKING SET) : 0.2958 REMARK 3 BIN FREE R VALUE : 0.3152 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.25 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 224 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 : 1029 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.63200 REMARK 3 B22 (A**2) : -6.63200 REMARK 3 B33 (A**2) : 13.26390 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) : 0.352 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.151 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.145 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.149 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.144 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 : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1134 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1579 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 373 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 30 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 190 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1134 ; 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 : 140 ; 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 : 1321 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.02 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.57 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.67 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 7MCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000255981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 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 : 13707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.82400 REMARK 200 FOR SHELL : 3.000 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: 3MXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% TACSIMATE, PH 7.0, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 41.63333 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 83.26667 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 83.26667 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 41.63333 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 GLY A 41 REMARK 465 GLU A 168 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 HIS A 42 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 64 CD OE1 NE2 REMARK 470 LYS A 99 CE NZ REMARK 470 LYS A 102 CE NZ REMARK 470 GLN A 127 CD OE1 NE2 REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 GLN A 159 CG CD OE1 NE2 REMARK 470 GLU A 167 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 ALA A 89 -4.66 -58.70 REMARK 500 ASN A 140 -165.69 -105.79 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 YWY A 301 DBREF 7MCE A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 7MCE GLY A 41 UNP O60885 EXPRESSION TAG SEQADV 7MCE HIS A 42 UNP O60885 EXPRESSION TAG SEQADV 7MCE MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 128 GLY HIS MET 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 YWY A 301 70 HETNAM YWY 2-{(7P)-7-(1,4-DIMETHYL-1H-1,2,3-TRIAZOL-5-YL)-8- HETNAM 2 YWY FLUORO-5-[(S)-(OXAN-4-YL)(PHENYL)METHYL]-5H-PYRIDO[3, HETNAM 3 YWY 2-B]INDOL-3-YL}PROPAN-2-OL FORMUL 2 YWY C30 H32 F N5 O2 FORMUL 3 HOH *34(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 GLU A 163 1 20 SITE 1 AC1 15 TRP A 81 PRO A 82 PHE A 83 VAL A 87 SITE 2 AC1 15 LYS A 91 LEU A 92 ASN A 130 PHE A 133 SITE 3 AC1 15 ASN A 140 ASP A 145 MET A 149 GLU A 154 SITE 4 AC1 15 HOH A 401 HOH A 404 HOH A 415 CRYST1 42.500 42.500 124.900 90.00 90.00 120.00 P 31 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 0.023529 0.013585 0.000000 0.00000 SCALE2 0.000000 0.027169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008006 0.00000