HEADER TRANSCRIPTION 09-JUN-16 5L98 TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH 3-AMINO-2- TITLE 2 METHYLPYRIDINE DERIVATIVE 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (RESIDUES 2054-2168); COMPND 5 SYNONYM: HWALP4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAZ2B, KIAA1476; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.LOLLI,J.-R.MARCHAND,A.CAFLISCH REVDAT 3 10-JAN-24 5L98 1 REMARK REVDAT 2 21-DEC-16 5L98 1 JRNL REVDAT 1 26-OCT-16 5L98 0 JRNL AUTH J.R.MARCHAND,G.LOLLI,A.CAFLISCH JRNL TITL DERIVATIVES OF 3-AMINO-2-METHYLPYRIDINE AS BAZ2B BROMODOMAIN JRNL TITL 2 LIGANDS: IN SILICO DISCOVERY AND IN CRYSTALLO VALIDATION. JRNL REF J. MED. CHEM. V. 59 9919 2016 JRNL REFN ISSN 1520-4804 JRNL PMID 27731638 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01258 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 10703 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.530 REMARK 3 FREE R VALUE TEST SET COUNT : 592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.2079 - 3.5921 1.00 2644 145 0.1688 0.1880 REMARK 3 2 3.5921 - 2.8512 1.00 2508 157 0.2271 0.2572 REMARK 3 3 2.8512 - 2.4908 0.98 2472 154 0.2563 0.2861 REMARK 3 4 2.4908 - 2.2631 0.99 2487 136 0.2560 0.3183 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1003 REMARK 3 ANGLE : 1.111 1347 REMARK 3 CHIRALITY : 0.040 143 REMARK 3 PLANARITY : 0.004 169 REMARK 3 DIHEDRAL : 14.990 385 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1856 THROUGH 1868 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1881 -34.3222 -9.6708 REMARK 3 T TENSOR REMARK 3 T11: 0.4840 T22: 0.7369 REMARK 3 T33: 0.7316 T12: -0.0012 REMARK 3 T13: 0.1003 T23: 0.0458 REMARK 3 L TENSOR REMARK 3 L11: 1.5704 L22: 0.2919 REMARK 3 L33: 0.0887 L12: 0.6809 REMARK 3 L13: 0.3767 L23: 0.1714 REMARK 3 S TENSOR REMARK 3 S11: -0.3373 S12: -0.9034 S13: -0.5659 REMARK 3 S21: -0.0980 S22: -0.1453 S23: 0.5398 REMARK 3 S31: -0.5212 S32: 0.1894 S33: 0.5389 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3764 -17.5650 -4.1283 REMARK 3 T TENSOR REMARK 3 T11: 0.3352 T22: 0.3415 REMARK 3 T33: 0.3389 T12: -0.0006 REMARK 3 T13: -0.0354 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.8281 L22: 1.9433 REMARK 3 L33: 1.8451 L12: -0.4469 REMARK 3 L13: 0.0391 L23: 0.4979 REMARK 3 S TENSOR REMARK 3 S11: 0.0518 S12: 0.0186 S13: -0.1324 REMARK 3 S21: -0.1556 S22: 0.0097 S23: 0.1083 REMARK 3 S31: -0.1528 S32: 0.0231 S33: -0.0912 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7104 -19.7396 7.2434 REMARK 3 T TENSOR REMARK 3 T11: 0.5689 T22: 0.5048 REMARK 3 T33: 0.3988 T12: 0.0643 REMARK 3 T13: -0.0839 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 1.9488 L22: 4.6053 REMARK 3 L33: 2.6531 L12: -0.6004 REMARK 3 L13: -0.2172 L23: 0.3870 REMARK 3 S TENSOR REMARK 3 S11: -0.3836 S12: -0.5030 S13: -0.1112 REMARK 3 S21: 1.1361 S22: 0.3328 S23: -0.2185 REMARK 3 S31: 0.1690 S32: 0.3197 S33: -0.0689 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5L98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R 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 PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10776 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 48.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 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: PHASER REMARK 200 STARTING MODEL: 4IR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG500MME (20%), PEG1000 (2%), PEG3350 REMARK 280 (2%), PEG20000 (10%), MPD (2%), PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 28.80650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.80650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 40.25150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.19700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.25150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.19700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.80650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.25150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.19700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.80650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.25150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.19700 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7920 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 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 ARG A1864 144.31 -39.10 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 6RY A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E9K RELATED DB: PDB REMARK 900 5E9K CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR HEAD GROUP. REMARK 900 RELATED ID: 5L8T RELATED DB: PDB REMARK 900 5L8T CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR COMPOUND. REMARK 900 RELATED ID: 5L8U RELATED DB: PDB REMARK 900 5L8U CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR COMPOUND. REMARK 900 RELATED ID: 5L96 RELATED DB: PDB REMARK 900 5L96 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR COMPOUND. REMARK 900 RELATED ID: 5L97 RELATED DB: PDB REMARK 900 5L97 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR COMPOUND. DBREF 5L98 A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 1858 1971 SEQADV 5L98 SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5L98 MET A 1857 UNP Q9UIF8 EXPRESSION TAG SEQRES 1 A 116 SER MET SER VAL LYS LYS PRO LYS ARG ASP ASP SER LYS SEQRES 2 A 116 ASP LEU ALA LEU CYS SER MET ILE LEU THR GLU MET GLU SEQRES 3 A 116 THR HIS GLU ASP ALA TRP PRO PHE LEU LEU PRO VAL ASN SEQRES 4 A 116 LEU LYS LEU VAL PRO GLY TYR LYS LYS VAL ILE LYS LYS SEQRES 5 A 116 PRO MET ASP PHE SER THR ILE ARG GLU LYS LEU SER SER SEQRES 6 A 116 GLY GLN TYR PRO ASN LEU GLU THR PHE ALA LEU ASP VAL SEQRES 7 A 116 ARG LEU VAL PHE ASP ASN CYS GLU THR PHE ASN GLU ASP SEQRES 8 A 116 ASP SER ASP ILE GLY ARG ALA GLY HIS ASN MET ARG LYS SEQRES 9 A 116 TYR PHE GLU LYS LYS TRP THR ASP THR PHE LYS VAL HET 6RY A2001 20 HET EDO A2002 4 HET EDO A2003 4 HETNAM 6RY ~{N}-[(1~{S})-1-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL) HETNAM 2 6RY ETHYL]-2-METHYL-PYRIDIN-3-AMINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 6RY C16 H18 N2 O2 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *42(H2 O) HELIX 1 AA1 LYS A 1868 HIS A 1883 1 16 HELIX 2 AA2 GLU A 1884 LEU A 1890 5 7 HELIX 3 AA3 GLY A 1900 ILE A 1905 1 6 HELIX 4 AA4 ASP A 1910 SER A 1920 1 11 HELIX 5 AA5 ASN A 1925 ASN A 1944 1 20 HELIX 6 AA6 SER A 1948 PHE A 1969 1 22 SITE 1 AC1 8 TRP A1887 PRO A1888 VAL A1893 PHE A1943 SITE 2 AC1 8 ASN A1944 EDO A2002 EDO A2003 HOH A2108 SITE 1 AC2 1 6RY A2001 SITE 1 AC3 2 PRO A1899 6RY A2001 CRYST1 80.503 96.394 57.613 90.00 90.00 90.00 C 2 2 21 8 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 0.012422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017357 0.00000