HEADER TRANSCRIPTION/INHIBITOR 01-MAR-21 7LWF TITLE CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH OICR-9320 COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-CELL LYMPHOMA 6 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BTB DOMAIN, RESIDUES 5-129; COMPND 5 SYNONYM: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC COMPND 6 FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51; COMPND 7 ENGINEERED: YES; COMPND 8 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: BCL6, BCL5, LAZ3, ZBTB27, ZNF51; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS IMMUNITY, INFLAMMATORY RESPONSE, TRANSCRIPTION REPRESSOR, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.A.KUNTZ,G.G.PRIVE REVDAT 4 25-OCT-23 7LWF 1 REMARK REVDAT 3 01-MAR-23 7LWF 1 JRNL REVDAT 2 25-JAN-23 7LWF 1 JRNL REVDAT 1 09-MAR-22 7LWF 0 JRNL AUTH A.MAMAI,A.M.CHAU,B.J.WILSON,I.D.WATSON,B.B.JOSEPH, JRNL AUTH 2 P.R.SUBRAMANIAN,M.M.MORSHED,J.A.MORIN,M.A.PRAKESCH,T.LU, JRNL AUTH 3 P.CONNOLLY,D.A.KUNTZ,N.C.POMROY,G.PODA,K.NGUYEN,R.MARCELLUS, JRNL AUTH 4 G.STRATHDEE,B.THERIAULT,R.SUBRAMANIAM,M.MOHAMMED,A.ABIBI, JRNL AUTH 5 M.CHAN,J.WINSTON,T.KIYOTA,E.UNDZYS,A.AMAN,N.AUSTIN, JRNL AUTH 6 M.DU JARDIN,K.PACKMAN,U.PHILLIPPAR,R.ATTAR,J.EDWARDS, JRNL AUTH 7 J.O'MEARA,D.E.UEHLING,R.AL-AWAR,G.G.PRIVE,M.B.ISAAC JRNL TITL DISCOVERY OF OICR12694: A NOVEL, POTENT, SELECTIVE, AND JRNL TITL 2 ORALLY BIOAVAILABLE BCL6 BTB INHIBITOR. JRNL REF ACS MED.CHEM.LETT. V. 14 199 2023 JRNL REFN ISSN 1948-5875 JRNL PMID 36793435 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00502 REMARK 2 REMARK 2 RESOLUTION. 1.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 34148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1734 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 29.9600 - 2.7900 0.97 2655 170 0.1436 0.1708 REMARK 3 2 2.7900 - 2.2200 0.98 2689 139 0.1373 0.1417 REMARK 3 3 2.2200 - 1.9400 0.99 2713 137 0.1236 0.1374 REMARK 3 4 1.9400 - 1.7600 1.00 2734 153 0.1291 0.1470 REMARK 3 5 1.7600 - 1.6300 1.00 2681 154 0.1311 0.1660 REMARK 3 6 1.6300 - 1.5400 1.00 2743 109 0.1341 0.1461 REMARK 3 7 1.5400 - 1.4600 1.00 2696 128 0.1445 0.1739 REMARK 3 8 1.4600 - 1.4000 1.00 2736 140 0.1690 0.1995 REMARK 3 9 1.4000 - 1.3400 1.00 2703 139 0.1881 0.2367 REMARK 3 10 1.3400 - 1.3000 1.00 2702 155 0.2024 0.2379 REMARK 3 11 1.3000 - 1.2600 0.99 2687 173 0.2328 0.2585 REMARK 3 12 1.2600 - 1.2200 1.00 2675 137 0.2661 0.2591 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) : 0.118 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.062 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 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 : 0.012 1098 REMARK 3 ANGLE : 1.540 1491 REMARK 3 CHIRALITY : 0.098 168 REMARK 3 PLANARITY : 0.010 190 REMARK 3 DIHEDRAL : 20.919 418 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 7LWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 36.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 3LBZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, CITRATE COCRYSTALLIZATION, REMARK 280 CRYSTAL SOAKED WITH HEPES PH 7.4, 20% GLYCEROL, LIGAND PRIOR TO REMARK 280 FREEZING., PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 15.23650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.23650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.21000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 15.60934 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -53.35559 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 O2 GOL A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 345 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 375 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 397 LIES ON A SPECIAL POSITION. 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 ALA A 5 REMARK 465 ASP A 6 REMARK 465 GLU A 129 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 SER A 39 -112.59 54.72 REMARK 500 SER A 39 -113.56 57.37 REMARK 500 GLN A 113 60.47 60.37 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 YNA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 DBREF 7LWF A 5 129 UNP P41182 BCL6_HUMAN 5 129 SEQADV 7LWF GLN A 8 UNP P41182 CYS 8 ENGINEERED MUTATION SEQADV 7LWF ARG A 67 UNP P41182 CYS 67 ENGINEERED MUTATION SEQADV 7LWF ASN A 84 UNP P41182 CYS 84 ENGINEERED MUTATION SEQRES 1 A 125 ALA ASP SER GLN ILE GLN PHE THR ARG HIS ALA SER ASP SEQRES 2 A 125 VAL LEU LEU ASN LEU ASN ARG LEU ARG SER ARG ASP ILE SEQRES 3 A 125 LEU THR ASP VAL VAL ILE VAL VAL SER ARG GLU GLN PHE SEQRES 4 A 125 ARG ALA HIS LYS THR VAL LEU MET ALA CYS SER GLY LEU SEQRES 5 A 125 PHE TYR SER ILE PHE THR ASP GLN LEU LYS ARG ASN LEU SEQRES 6 A 125 SER VAL ILE ASN LEU ASP PRO GLU ILE ASN PRO GLU GLY SEQRES 7 A 125 PHE ASN ILE LEU LEU ASP PHE MET TYR THR SER ARG LEU SEQRES 8 A 125 ASN LEU ARG GLU GLY ASN ILE MET ALA VAL MET ALA THR SEQRES 9 A 125 ALA MET TYR LEU GLN MET GLU HIS VAL VAL ASP THR CYS SEQRES 10 A 125 ARG LYS PHE ILE LYS ALA SER GLU HET YNA A 201 45 HET GOL A 202 13 HETNAM YNA N-(3-CHLOROPYRIDIN-4-YL)-2-[5-(3-CYANO-4- HETNAM 2 YNA HYDROXYPHENYL)-3-METHYL-4-OXO-3,4-DIHYDRO-7H- HETNAM 3 YNA PYRROLO[2,3-D]PYRIMIDIN-7-YL]ACETAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 YNA C21 H15 CL N6 O3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *135(H2 O) HELIX 1 AA1 ARG A 13 ARG A 28 1 16 HELIX 2 AA2 HIS A 46 SER A 54 1 9 HELIX 3 AA3 SER A 54 ASP A 63 1 10 HELIX 4 AA4 ASN A 79 SER A 93 1 15 HELIX 5 AA5 ASN A 101 GLN A 113 1 13 HELIX 6 AA6 MET A 114 ALA A 127 1 14 SHEET 1 AA1 3 GLU A 41 ALA A 45 0 SHEET 2 AA1 3 VAL A 34 VAL A 38 -1 N ILE A 36 O PHE A 43 SHEET 3 AA1 3 VAL A 71 ASN A 73 1 O ILE A 72 N VAL A 37 SITE 1 AC1 21 HIS A 14 ASN A 21 ARG A 24 LEU A 25 SITE 2 AC1 21 MET A 51 ALA A 52 CYS A 53 SER A 54 SITE 3 AC1 21 GLY A 55 TYR A 58 PHE A 89 GLN A 113 SITE 4 AC1 21 MET A 114 GLU A 115 HIS A 116 VAL A 117 SITE 5 AC1 21 HOH A 355 HOH A 363 HOH A 373 HOH A 389 SITE 6 AC1 21 HOH A 431 SITE 1 AC2 4 LEU A 31 ASP A 33 LYS A 47 THR A 48 CRYST1 30.473 72.420 55.592 90.00 106.31 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 0.032816 0.000000 0.009600 0.00000 SCALE2 0.000000 0.013808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018742 0.00000