HEADER PROTEIN BINDING 04-NOV-21 7Q5O TITLE BROMODOMAIN-CONTAINING 2 BD2 IN COMPLEX WITH THE INHIBITOR CRCM5484 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS EPIGENETIC, INHIBITION, INHIBITOR, SELECTIVITY, COMPLEX, BDII, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.CARRASCO,S.BETZI,X.MORELLI REVDAT 2 31-JAN-24 7Q5O 1 REMARK REVDAT 1 20-APR-22 7Q5O 0 JRNL AUTH K.CARRASCO,C.MONTERSINO,C.DERVIAUX,M.SAEZ-AYALA,L.HOFFER, JRNL AUTH 2 A.RESTOUIN,R.CASTELLANO,J.CASASSA,P.ROCHE,E.PASQUIER, JRNL AUTH 3 S.COMBES,X.MORELLI,Y.COLLETTE,S.BETZI JRNL TITL CRCM5484: A BET-BDII SELECTIVE COMPOUND WITH DIFFERENTIAL JRNL TITL 2 ANTI-LEUKEMIC DRUG MODULATION JRNL REF J.MED.CHEM. V. 65 5660 2022 JRNL REFN ISSN 0022-2623 JRNL DOI 10.1021/ACS.JMEDCHEM.1C02168 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 19121 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 877 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 29.8160 - 2.7593 0.98 3206 168 0.1704 0.1987 REMARK 3 2 2.7593 - 2.1904 0.98 3048 140 0.2016 0.2617 REMARK 3 3 2.1904 - 1.9135 0.99 3080 140 0.2211 0.2605 REMARK 3 4 1.9135 - 1.7386 0.99 3034 151 0.2515 0.2557 REMARK 3 5 1.7386 - 1.6140 0.98 2945 160 0.2784 0.3054 REMARK 3 6 1.6140 - 1.5190 0.96 2931 118 0.3296 0.3169 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.95 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 345 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.6232 2.3221 15.1009 REMARK 3 T TENSOR REMARK 3 T11: 0.0461 T22: 0.0581 REMARK 3 T33: 0.0565 T12: 0.0128 REMARK 3 T13: 0.0029 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.0534 L22: 2.2157 REMARK 3 L33: 0.5304 L12: 0.1978 REMARK 3 L13: -0.0197 L23: 0.1941 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: 0.0346 S13: 0.0487 REMARK 3 S21: 0.0990 S22: 0.0268 S23: 0.0780 REMARK 3 S31: -0.0070 S32: -0.0321 S33: -0.0243 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 7Q5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 275 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.885602 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.519 REMARK 200 RESOLUTION RANGE LOW (A) : 29.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.17960 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90460 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: 5XHK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 100 MM POTASSIUM REMARK 280 THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 26.21500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.21500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.24700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6820 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 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 HOH A 755 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 759 LIES ON A SPECIAL POSITION. 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 704 O HOH A 746 1.86 REMARK 500 NZ LYS A 364 O HOH A 601 2.04 REMARK 500 O HOH A 706 O HOH A 754 2.08 REMARK 500 O HOH A 634 O HOH A 691 2.09 REMARK 500 O HOH A 648 O HOH A 656 2.12 REMARK 500 O HOH A 705 O HOH A 728 2.15 REMARK 500 NH1 ARG A 401 O HOH A 602 2.19 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 658 O HOH A 679 1554 2.19 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 A 759 DISTANCE = 6.41 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7Q3F RELATED DB: PDB DBREF 7Q5O A 346 454 UNP P25440 BRD2_HUMAN 346 454 SEQADV 7Q5O ALA A 345 UNP P25440 EXPRESSION TAG SEQRES 1 A 110 ALA LEU SER GLU GLN LEU LYS HIS CYS ASN GLY ILE LEU SEQRES 2 A 110 LYS GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 110 PRO PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY LEU SEQRES 4 A 110 HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP LEU SEQRES 5 A 110 SER THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR ARG SEQRES 6 A 110 ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 110 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP VAL SEQRES 8 A 110 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU PHE SEQRES 9 A 110 ARG TYR ALA LYS MET PRO HET 8M6 A 501 35 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HETNAM 8M6 2-[[11-ETHANOYL-4-(FURAN-2-YLMETHYL)-3-OXIDANYLIDENE-8- HETNAM 2 8M6 THIA-4,6,11-TRIAZATRICYCLO[7.4.0.0^{2,7}]TRIDECA-1(9), HETNAM 3 8M6 2(7),5-TRIEN-5-YL]SULFANYL]-~{N}-(2-METHYLPYRIDIN-3- HETNAM 4 8M6 YL)ETHANAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8M6 C24 H23 N5 O4 S2 FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *159(H2 O) HELIX 1 AA1 SER A 347 LEU A 361 1 15 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 385 ILE A 390 1 6 HELIX 6 AA6 ASP A 395 ASN A 405 1 11 HELIX 7 AA7 ASP A 410 ASN A 429 1 20 HELIX 8 AA8 HIS A 433 ALA A 451 1 19 CRYST1 52.430 72.494 32.041 90.00 90.00 90.00 P 21 21 2 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 0.019073 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031210 0.00000