HEADER GENE REGULATION/INHIBITOR 20-AUG-21 7RWN TITLE CRYSTAL STRUCTURE OF BPTF BROMODOMAIN IN COMPLEX WITH 4-CHLORO-5-{4- TITLE 2 [(DIMETHYLAMINO)METHYL]ANILINO}-2-METHYLPYRIDAZIN-3(2H)-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR, COMPND 5 FETAL ALZ-50 CLONE 1 PROTEIN,FETAL ALZHEIMER ANTIGEN; COMPND 6 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, FAC1, FALZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BRD4, GENE REGULATION, GENE REGULATION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZAHID,C.BUCHHOLZ,J.A.JOHNSON,K.SHI,H.AIHARA,W.C.K.POMERANTZ REVDAT 3 18-OCT-23 7RWN 1 REMARK REVDAT 2 19-OCT-22 7RWN 1 JRNL REVDAT 1 24-AUG-22 7RWN 0 JRNL AUTH H.ZAHID,C.R.BUCHHOLZ,M.SINGH,M.F.CICCONE,A.CHAN, JRNL AUTH 2 S.NITHIANANTHAM,K.SHI,H.AIHARA,M.FISCHER,E.SCHONBRUNN, JRNL AUTH 3 C.O.DOS SANTOS,J.W.LANDRY,W.C.K.POMERANTZ JRNL TITL NEW DESIGN RULES FOR DEVELOPING POTENT CELL-ACTIVE JRNL TITL 2 INHIBITORS OF THE NUCLEOSOME REMODELING FACTOR (NURF) VIA JRNL TITL 3 BPTF BROMODOMAIN INHIBITION. JRNL REF J.MED.CHEM. V. 64 13902 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34515477 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01294 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 27062 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1298 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 38.2800 - 2.8900 0.97 2899 125 0.1527 0.1697 REMARK 3 2 2.8800 - 2.2900 0.98 2910 119 0.1501 0.1747 REMARK 3 3 2.2900 - 2.0000 0.98 2842 163 0.1280 0.1757 REMARK 3 4 2.0000 - 1.8200 0.98 2858 145 0.1408 0.1849 REMARK 3 5 1.8200 - 1.6900 0.99 2928 131 0.1296 0.1665 REMARK 3 6 1.6900 - 1.5900 0.98 2861 143 0.1315 0.1802 REMARK 3 7 1.5900 - 1.5100 0.99 2870 164 0.1429 0.2081 REMARK 3 8 1.5100 - 1.4400 0.99 2850 169 0.1492 0.1847 REMARK 3 9 1.4400 - 1.3900 0.94 2746 139 0.1725 0.2136 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.94 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7RWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-20 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 : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : M REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 66.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 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: 7JT4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MANGANESE ACETATE AND 2% (V/V) REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.42700 REMARK 290 SMTRY3 2 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 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 2907 REMARK 465 THR A 2908 REMARK 465 GLU A 2909 REMARK 465 ASN A 2910 REMARK 465 LEU A 2911 REMARK 465 TYR A 2912 REMARK 465 PHE A 2913 REMARK 465 GLN A 2914 REMARK 465 SER A 2915 REMARK 465 MET A 2916 REMARK 465 SER A 2917 REMARK 465 THR A 2918 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 O HOH A 3206 O HOH A 3330 1.81 REMARK 500 O HOH A 3261 O HOH A 3274 1.84 REMARK 500 O HOH A 3208 O HOH A 3211 1.85 REMARK 500 O HOH A 3331 O HOH A 3337 1.96 REMARK 500 O HOH A 3258 O HOH A 3402 1.98 REMARK 500 O HOH A 3349 O HOH A 3390 1.98 REMARK 500 N GLU A 2919 O HOH A 3201 2.01 REMARK 500 O HOH A 3360 O HOH A 3420 2.04 REMARK 500 O HOH A 3294 O HOH A 3393 2.06 REMARK 500 O HOH A 3322 O HOH A 3365 2.11 REMARK 500 OG SER A 3034 O HOH A 3202 2.11 REMARK 500 O HOH A 3331 O HOH A 3333 2.13 REMARK 500 O HOH A 3306 O HOH A 3334 2.15 REMARK 500 NH1 ARG A 2983 O HOH A 3203 2.16 REMARK 500 O HOH A 3205 O HOH A 3350 2.18 REMARK 500 OE1 GLU A 2954 O HOH A 3204 2.18 REMARK 500 OE2 GLU A 2934 NH1 ARG A 2938 2.18 REMARK 500 O HIS A 3037 O HOH A 3205 2.18 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 3205 O HOH A 3209 2655 2.06 REMARK 500 O HOH A 3265 O HOH A 3306 1455 2.16 REMARK 500 O HOH A 3208 O HOH A 3210 1455 2.17 REMARK 500 O HOH A 3205 O HOH A 3230 2655 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 A2961 76.91 -159.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A3435 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A3436 DISTANCE = 7.69 ANGSTROMS DBREF 7RWN A 2917 3037 UNP Q12830 BPTF_HUMAN 2917 3037 SEQADV 7RWN GLY A 2907 UNP Q12830 EXPRESSION TAG SEQADV 7RWN THR A 2908 UNP Q12830 EXPRESSION TAG SEQADV 7RWN GLU A 2909 UNP Q12830 EXPRESSION TAG SEQADV 7RWN ASN A 2910 UNP Q12830 EXPRESSION TAG SEQADV 7RWN LEU A 2911 UNP Q12830 EXPRESSION TAG SEQADV 7RWN TYR A 2912 UNP Q12830 EXPRESSION TAG SEQADV 7RWN PHE A 2913 UNP Q12830 EXPRESSION TAG SEQADV 7RWN GLN A 2914 UNP Q12830 EXPRESSION TAG SEQADV 7RWN SER A 2915 UNP Q12830 EXPRESSION TAG SEQADV 7RWN MET A 2916 UNP Q12830 EXPRESSION TAG SEQRES 1 A 131 GLY THR GLU ASN LEU TYR PHE GLN SER MET SER THR GLU SEQRES 2 A 131 ASP ALA MET THR VAL LEU THR PRO LEU THR GLU LYS ASP SEQRES 3 A 131 TYR GLU GLY LEU LYS ARG VAL LEU ARG SER LEU GLN ALA SEQRES 4 A 131 HIS LYS MET ALA TRP PRO PHE LEU GLU PRO VAL ASP PRO SEQRES 5 A 131 ASN ASP ALA PRO ASP TYR TYR GLY VAL ILE LYS GLU PRO SEQRES 6 A 131 MET ASP LEU ALA THR MET GLU GLU ARG VAL GLN ARG ARG SEQRES 7 A 131 TYR TYR GLU LYS LEU THR GLU PHE VAL ALA ASP MET THR SEQRES 8 A 131 LYS ILE PHE ASP ASN CYS ARG TYR TYR ASN PRO SER ASP SEQRES 9 A 131 SER PRO PHE TYR GLN CYS ALA GLU VAL LEU GLU SER PHE SEQRES 10 A 131 PHE VAL GLN LYS LEU LYS GLY PHE LYS ALA SER ARG SER SEQRES 11 A 131 HIS HET 7WE A3101 20 HET EDO A3102 4 HETNAM 7WE 4-CHLORO-5-{4-[(DIMETHYLAMINO)METHYL]ANILINO}-2- HETNAM 2 7WE METHYLPYRIDAZIN-3(2H)-ONE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 7WE C14 H17 CL N4 O FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *236(H2 O) HELIX 1 AA1 ASP A 2920 THR A 2926 1 7 HELIX 2 AA2 THR A 2929 HIS A 2946 1 18 HELIX 3 AA3 LYS A 2947 LEU A 2953 5 7 HELIX 4 AA4 ASP A 2957 ALA A 2961 5 5 HELIX 5 AA5 ASP A 2963 ILE A 2968 1 6 HELIX 6 AA6 ASP A 2973 ARG A 2983 1 11 HELIX 7 AA7 LYS A 2988 ASN A 3007 1 20 HELIX 8 AA8 SER A 3011 ARG A 3035 1 25 CRYST1 27.148 66.854 39.706 90.00 105.41 90.00 P 1 21 1 2 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 0.036835 0.000000 0.010150 0.00000 SCALE2 0.000000 0.014958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026124 0.00000