HEADER TRANSCRIPTION 22-JUL-26 32SN TITLE CRYSTAL STRUCTURE OF BRD4-BD1 IN COMPLEX WITH COMPOUND 13 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, INHIBITOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.BADER,D.KESSLER REVDAT 1 05-AUG-26 32SN 0 JRNL AUTH A.BEIER,G.PLATZER,T.HOFURTHNER,A.L.PTASZEK,R.J.LICHTENECKER, JRNL AUTH 2 L.GEIST,J.E.FUCHS,D.B.MCCONNELL,M.MAYER,R.KONRAT JRNL TITL PROBING PROTEIN-LIGAND METHYL-PI INTERACTION GEOMETRIES JRNL TITL 2 THROUGH CHEMICAL SHIFT MEASUREMENTS OF SELECTIVELY LABELED JRNL TITL 3 METHYL GROUPS. JRNL REF J MED CHEM V. 67 13187 2024 JRNL REFN ISSN 1520-4804 JRNL PMID 39069741 JRNL DOI 10.1039/B508541A REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 6846 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 301 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.27 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1445 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2248 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1385 REMARK 3 BIN R VALUE (WORKING SET) : 0.2207 REMARK 3 BIN FREE R VALUE : 0.3207 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.15 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 60 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 : 1059 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.48130 REMARK 3 B22 (A**2) : 8.78880 REMARK 3 B33 (A**2) : 1.69250 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) : 0.329 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.386 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.258 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.341 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.252 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 : 0.882 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.845 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1113 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1518 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 380 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 36 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 150 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1113 ; 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 : 139 ; 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 : 1355 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.92 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.76 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): 10.4463 3.6032 8.5762 REMARK 3 T TENSOR REMARK 3 T11: 0.1247 T22: -0.1039 REMARK 3 T33: -0.1569 T12: -0.0108 REMARK 3 T13: -0.0098 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 0.7167 L22: 1.8347 REMARK 3 L33: 2.1363 L12: 0.2421 REMARK 3 L13: 0.8445 L23: 0.5183 REMARK 3 S TENSOR REMARK 3 S11: -0.0955 S12: -0.0388 S13: 0.0613 REMARK 3 S21: -0.2105 S22: 0.0057 S23: 0.0229 REMARK 3 S31: -0.2761 S32: -0.0931 S33: 0.0898 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 32SN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-26. REMARK 100 THE DEPOSITION ID IS D_1292159174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.6 REMARK 200 DATA REDUNDANCY : 4.130 REMARK 200 R MERGE (I) : 0.09290 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25990 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37 % PEG 3350, 0.2 M SODIUM MALONATE, REMARK 280 0.01 M HEPES PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 17.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.85000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.85000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.40000 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 LYS A 141 CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 91 CG CD CE NZ REMARK 480 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 LEU A 94 73.93 -118.80 REMARK 500 THR A 103 76.10 -118.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 32PP RELATED DB: PDB REMARK 900 RELATED ID: 32SC RELATED DB: PDB REMARK 900 RELATED ID: 32RX RELATED DB: PDB REMARK 900 RELATED ID: 32RY RELATED DB: PDB REMARK 900 RELATED ID: 32RZ RELATED DB: PDB REMARK 900 RELATED ID: 32SB RELATED DB: PDB DBREF 32SN A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 32SN SER A 42 UNP O60885 EXPRESSION TAG SEQADV 32SN MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET KC3 A 201 17 HETNAM KC3 3-METHYL-6-(4-METHYLPIPERIDIN-1-YL)-[1,2,4]TRIAZOLO[4, HETNAM 2 KC3 3-B]PYRIDAZINE FORMUL 2 KC3 C12 H17 N5 FORMUL 3 HOH *61(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 CRYST1 34.000 46.800 77.700 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 0.029412 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012870 0.00000 CONECT 1066 1067 1077 CONECT 1067 1066 1069 1079 CONECT 1068 1070 1078 1081 CONECT 1069 1067 CONECT 1070 1068 1071 CONECT 1071 1070 1072 CONECT 1072 1071 1075 1076 CONECT 1073 1074 1078 1082 CONECT 1074 1073 CONECT 1075 1072 1077 1080 CONECT 1076 1072 1078 CONECT 1077 1066 1075 CONECT 1078 1068 1073 1076 CONECT 1079 1067 1080 CONECT 1080 1075 1079 CONECT 1081 1068 1082 CONECT 1082 1073 1081 MASTER 272 0 1 7 0 0 0 6 1137 1 17 10 END