HEADER DNA BINDING PROTEIN 13-FEB-23 8IDH TITLE BROMODOMAIN AND EXTRA-TERMINAL DOMAIN (BET) BRD4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BINDS ACETYLATED LYSINE RESIDUES, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.CAO,D.ZHIYAN,B.XIONG REVDAT 1 04-OCT-23 8IDH 0 JRNL AUTH X.CHEN,D.CAO,C.LIU,F.MENG,Z.ZHANG,R.XU,Y.TONG,Y.XIN,W.ZHANG, JRNL AUTH 2 W.KANG,Q.BAO,J.SHEN,B.XIONG,Q.YOU,Z.JIANG JRNL TITL DISCOVERY OF 1 H -IMIDAZO[4,5- B ]PYRIDINE DERIVATIVES AS JRNL TITL 2 POTENT AND SELECTIVE BET INHIBITORS FOR THE MANAGEMENT OF JRNL TITL 3 NEUROPATHIC PAIN. JRNL REF J.MED.CHEM. V. 66 8725 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 37382379 JRNL DOI 10.1021/ACS.JMEDCHEM.3C00372 REMARK 2 REMARK 2 RESOLUTION. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 27468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2763 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 18.0300 - 4.2500 0.99 1465 159 0.2130 0.2467 REMARK 3 2 4.2500 - 3.3800 0.99 1454 161 0.1929 0.2485 REMARK 3 3 3.3800 - 2.9600 0.99 1411 164 0.2274 0.2382 REMARK 3 4 2.9600 - 2.6900 0.99 1460 162 0.2370 0.2517 REMARK 3 5 2.6900 - 2.5000 0.98 1440 165 0.2127 0.2215 REMARK 3 6 2.5000 - 2.3500 0.98 1440 165 0.2217 0.2573 REMARK 3 7 2.3500 - 2.2300 0.98 1435 158 0.2166 0.2344 REMARK 3 8 2.2300 - 2.1300 0.99 1447 160 0.1991 0.2357 REMARK 3 9 2.1300 - 2.0500 0.99 1447 166 0.1962 0.2533 REMARK 3 10 2.0500 - 1.9800 0.99 1452 163 0.2020 0.2503 REMARK 3 11 1.9800 - 1.9200 0.99 1449 169 0.2148 0.2016 REMARK 3 12 1.9200 - 1.8600 0.97 1406 161 0.2304 0.2317 REMARK 3 13 1.8600 - 1.8200 0.96 1405 155 0.2389 0.2999 REMARK 3 14 1.8200 - 1.7700 0.89 1308 147 0.2580 0.2961 REMARK 3 15 1.7700 - 1.7300 0.77 1153 124 0.2824 0.3066 REMARK 3 16 1.7300 - 1.6900 0.66 944 106 0.2863 0.3069 REMARK 3 17 1.6900 - 1.6600 0.59 861 93 0.2906 0.3578 REMARK 3 18 1.6600 - 1.6300 0.47 698 77 0.3294 0.3733 REMARK 3 19 1.6300 - 1.6000 0.36 528 56 0.3216 0.3985 REMARK 3 20 1.6000 - 1.5700 0.34 502 52 0.3232 0.3751 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 967 REMARK 3 ANGLE : 1.236 1304 REMARK 3 CHIRALITY : 0.061 129 REMARK 3 PLANARITY : 0.009 166 REMARK 3 DIHEDRAL : 10.229 130 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 8IDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.1.012 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 42.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46200 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: PHENIX 1.19.2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL,0.1M BISTRIS,18-28%PEG3350, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 26.29550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.96450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.29550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.96450 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 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 607 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 674 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 367 CD CE NZ REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 LYS A 395 CG CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 CME A 356 REMARK 475 CME A 391 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 OE1 GLN A 416 O HOH A 601 1.87 REMARK 500 N ALA A 415 O HOH A 601 2.15 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 MET A 457 123.50 -31.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IDH A 349 460 UNP O60885 BRD4_HUMAN 349 460 SEQRES 1 A 112 LYS VAL SER GLU GLN LEU LYS CME CYS SER GLY ILE LEU SEQRES 2 A 112 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 112 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 A 112 HIS ASP TYR CME ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 A 112 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 A 112 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 112 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 112 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 112 ARG PHE ALA LYS MET PRO ASP GLU MODRES 8IDH CME A 356 CYS MODIFIED RESIDUE MODRES 8IDH CME A 391 CYS MODIFIED RESIDUE HET CME A 356 10 HET CME A 391 10 HET OWO A 501 40 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM OWO 7-[2-FLUORANYL-3-(1,3,5-TRIMETHYLPYRAZOL-4-YL)PHENYL]- HETNAM 2 OWO 1~{H}-IMIDAZO[4,5-B]PYRIDINE FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 OWO C18 H16 F N5 FORMUL 3 HOH *86(H2 O) HELIX 1 AA1 LYS A 349 PHE A 365 1 17 HELIX 2 AA2 ALA A 366 LYS A 368 5 3 HELIX 3 AA3 HIS A 369 TRP A 374 1 6 HELIX 4 AA4 PRO A 375 TYR A 377 5 3 HELIX 5 AA5 ASP A 381 GLY A 386 1 6 HELIX 6 AA6 ASP A 389 ILE A 394 1 6 HELIX 7 AA7 ASP A 399 ALA A 409 1 11 HELIX 8 AA8 ASP A 414 ASN A 433 1 20 HELIX 9 AA9 HIS A 437 ALA A 455 1 19 LINK C LYS A 355 N CME A 356 1555 1555 1.33 LINK C CME A 356 N CYS A 357 1555 1555 1.33 LINK C TYR A 390 N CME A 391 1555 1555 1.33 LINK C CME A 391 N ASP A 392 1555 1555 1.33 CRYST1 52.591 71.929 32.044 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 0.019015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031207 0.00000