HEADER ANTITUMOR PROTEIN 21-JUN-21 7F5E TITLE CRYSTAL STRUCTURE OF BPTF-BRD WITH LIGAND DC-BPI-11 BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF; COMPND 3 CHAIN: A; COMPND 4 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: BPTF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BPTF BROMODOMAIN, LYSINE ACETYLATION, SMALL-MOLECULE INHIBITOR, KEYWDS 2 BIOSYNTHETIC PROTEIN, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.LU,H.B.LU,J.WANG,H.LIN,W.LU,C.LUO REVDAT 2 29-NOV-23 7F5E 1 REMARK REVDAT 1 29-JUN-22 7F5E 0 JRNL AUTH T.LU,H.B.LU,J.WANG,J.HAN,S.XIAO,H.JIANG,Y.CHEN,F.YANG,Q.LI, JRNL AUTH 2 H.L.JIANG,K.X.CHEN,W.C.LU,H.LIN,C.LUO JRNL TITL DISCOVERY AND OPTIMIZATION OF SMALL-MOLECULE INHIBITORS FOR JRNL TITL 2 THE BPTF BROMODOMAINS PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 5770 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.338 REMARK 3 FREE R VALUE TEST SET COUNT : 308 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 3.5000 - 2.7717 1.00 2905 152 0.1846 0.2573 REMARK 3 2 2.7717 - 2.2002 0.91 2557 156 0.1939 0.3044 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.306 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.561 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.19 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 : 0.009 1009 REMARK 3 ANGLE : 0.967 1380 REMARK 3 CHIRALITY : 0.046 139 REMARK 3 PLANARITY : 0.005 176 REMARK 3 DIHEDRAL : 18.171 622 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7F5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5770 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53700 REMARK 200 R SYM FOR SHELL (I) : 0.53700 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: 3QZT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M TRIS PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.72400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.57850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.72400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.57850 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 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 PRO A 61 REMARK 465 LEU A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 VAL A 65 REMARK 465 ALA A 174 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 79 O HOH A 301 1.90 REMARK 500 NZ LYS A 129 O HOH A 302 1.91 REMARK 500 NH2 ARG A 79 O HOH A 303 1.95 REMARK 500 O HOH A 348 O HOH A 349 2.00 REMARK 500 O HOH A 347 O HOH A 348 2.05 REMARK 500 O HOH A 348 O HOH A 352 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 328 O HOH A 340 4546 1.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 7F5E A 65 174 UNP J3QQQ8 J3QQQ8_HUMAN 308 417 SEQADV 7F5E PRO A 61 UNP J3QQQ8 EXPRESSION TAG SEQADV 7F5E LEU A 62 UNP J3QQQ8 EXPRESSION TAG SEQADV 7F5E GLY A 63 UNP J3QQQ8 EXPRESSION TAG SEQADV 7F5E SER A 64 UNP J3QQQ8 EXPRESSION TAG SEQRES 1 A 114 PRO LEU GLY SER VAL LEU THR PRO LEU THR GLU LYS ASP SEQRES 2 A 114 TYR GLU GLY LEU LYS ARG VAL LEU ARG SER LEU GLN ALA SEQRES 3 A 114 HIS LYS MET ALA TRP PRO PHE LEU GLU PRO VAL ASP PRO SEQRES 4 A 114 ASN ASP ALA PRO ASP TYR TYR GLY VAL ILE LYS GLU PRO SEQRES 5 A 114 MET ASP LEU ALA THR MET GLU GLU ARG VAL GLN ARG ARG SEQRES 6 A 114 TYR TYR GLU LYS LEU THR GLU PHE VAL ALA ASP MET THR SEQRES 7 A 114 LYS ILE PHE ASP ASN CYS ARG TYR TYR ASN PRO SER ASP SEQRES 8 A 114 SER PRO PHE TYR GLN CYS ALA GLU VAL LEU GLU SER PHE SEQRES 9 A 114 PHE VAL GLN LYS LEU LYS GLY PHE LYS ALA HET 1IY A 201 50 HETNAM 1IY N,N-DIMETHYL-3-[5-(2-METHYLSULFONYL-7H-PYRROLO[2,3- HETNAM 2 1IY D]PYRIMIDIN-4-YL)INDOL-1-YL]PROPAN-1-AMINE FORMUL 2 1IY C20 H23 N5 O2 S FORMUL 3 HOH *52(H2 O) HELIX 1 AA1 THR A 70 HIS A 87 1 18 HELIX 2 AA2 LYS A 88 LEU A 94 5 7 HELIX 3 AA3 ASP A 98 ALA A 102 5 5 HELIX 4 AA4 ASP A 104 ILE A 109 1 6 HELIX 5 AA5 ASP A 114 ARG A 124 1 11 HELIX 6 AA6 LYS A 129 ASN A 148 1 20 HELIX 7 AA7 SER A 152 LYS A 173 1 22 CRYST1 111.448 27.157 38.697 90.00 98.53 90.00 C 1 2 1 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 0.008973 0.000000 0.001346 0.00000 SCALE2 0.000000 0.036823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026131 0.00000