HEADER TRANSCRIPTION 11-SEP-18 6HM0 TITLE CRYSTAL STRUCTURE OF HUMAN BRD9 BROMODOMAIN IN COMPLEX WITH A PROTAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8; 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: BRD9, UNQ3040/PRO9856; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTAC, LYSINE-ACETYLATED HISTONE BINDING, CHROMATIN REGULATOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.J.HUGHES,V.ZOPPI,A.CIULLI REVDAT 3 24-JAN-24 6HM0 1 REMARK REVDAT 2 24-APR-19 6HM0 1 JRNL REVDAT 1 16-JAN-19 6HM0 0 JRNL AUTH V.ZOPPI,S.J.HUGHES,C.MANIACI,A.TESTA,T.GMASCHITZ, JRNL AUTH 2 C.WIESHOFER,M.KOEGL,K.M.RICHING,D.L.DANIELS,A.SPALLAROSSA, JRNL AUTH 3 A.CIULLI JRNL TITL ITERATIVE DESIGN AND OPTIMIZATION OF INITIALLY INACTIVE JRNL TITL 2 PROTEOLYSIS TARGETING CHIMERAS (PROTACS) IDENTIFY VZ185 AS A JRNL TITL 3 POTENT, FAST, AND SELECTIVE VON HIPPEL-LINDAU (VHL) BASED JRNL TITL 4 DUAL DEGRADER PROBE OF BRD9 AND BRD7. JRNL REF J.MED.CHEM. V. 62 699 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 30540463 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01413 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 9627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 556 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : 2.39000 REMARK 3 B33 (A**2) : -0.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.556 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.278 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.402 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6HM0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-17 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10196 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 41.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 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: MOLREP REMARK 200 STARTING MODEL: 5I40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3350 0.2 M NH4F, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 29.91000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 12 REMARK 465 MET A 13 REMARK 465 LEU A 14 REMARK 465 LYS A 15 REMARK 465 LEU A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 GLU A 19 REMARK 465 ASN A 20 REMARK 465 GLU A 21 REMARK 465 SER A 134 REMARK 465 SER B 12 REMARK 465 MET B 13 REMARK 465 LEU B 14 REMARK 465 LYS B 15 REMARK 465 LEU B 16 REMARK 465 SER B 17 REMARK 465 ALA B 18 REMARK 465 GLU B 19 REMARK 465 ASN B 20 REMARK 465 GLU B 21 REMARK 465 SER B 134 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 ASP A 103 30.22 -88.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GBW A 201 REMARK 610 GBW B 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GBW A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GBW B 201 DBREF 6HM0 A 14 134 UNP Q9H8M2 BRD9_HUMAN 14 134 DBREF 6HM0 B 14 134 UNP Q9H8M2 BRD9_HUMAN 14 134 SEQADV 6HM0 SER A 12 UNP Q9H8M2 EXPRESSION TAG SEQADV 6HM0 MET A 13 UNP Q9H8M2 EXPRESSION TAG SEQADV 6HM0 SER B 12 UNP Q9H8M2 EXPRESSION TAG SEQADV 6HM0 MET B 13 UNP Q9H8M2 EXPRESSION TAG SEQRES 1 A 123 SER MET LEU LYS LEU SER ALA GLU ASN GLU SER THR PRO SEQRES 2 A 123 ILE GLN GLN LEU LEU GLU HIS PHE LEU ARG GLN LEU GLN SEQRES 3 A 123 ARG LYS ASP PRO HIS GLY PHE PHE ALA PHE PRO VAL THR SEQRES 4 A 123 ASP ALA ILE ALA PRO GLY TYR SER MET ILE ILE LYS HIS SEQRES 5 A 123 PRO MET ASP PHE GLY THR MET LYS ASP LYS ILE VAL ALA SEQRES 6 A 123 ASN GLU TYR LYS SER VAL THR GLU PHE LYS ALA ASP PHE SEQRES 7 A 123 LYS LEU MET CYS ASP ASN ALA MET THR TYR ASN ARG PRO SEQRES 8 A 123 ASP THR VAL TYR TYR LYS LEU ALA LYS LYS ILE LEU HIS SEQRES 9 A 123 ALA GLY PHE LYS MET MET SER LYS GLU ARG LEU LEU ALA SEQRES 10 A 123 LEU LYS ARG SER MET SER SEQRES 1 B 123 SER MET LEU LYS LEU SER ALA GLU ASN GLU SER THR PRO SEQRES 2 B 123 ILE GLN GLN LEU LEU GLU HIS PHE LEU ARG GLN LEU GLN SEQRES 3 B 123 ARG LYS ASP PRO HIS GLY PHE PHE ALA PHE PRO VAL THR SEQRES 4 B 123 ASP ALA ILE ALA PRO GLY TYR SER MET ILE ILE LYS HIS SEQRES 5 B 123 PRO MET ASP PHE GLY THR MET LYS ASP LYS ILE VAL ALA SEQRES 6 B 123 ASN GLU TYR LYS SER VAL THR GLU PHE LYS ALA ASP PHE SEQRES 7 B 123 LYS LEU MET CYS ASP ASN ALA MET THR TYR ASN ARG PRO SEQRES 8 B 123 ASP THR VAL TYR TYR LYS LEU ALA LYS LYS ILE LEU HIS SEQRES 9 B 123 ALA GLY PHE LYS MET MET SER LYS GLU ARG LEU LEU ALA SEQRES 10 B 123 LEU LYS ARG SER MET SER HET GBW A 201 33 HET GBW B 201 33 HETNAM GBW (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-DIMETHOXY- HETNAM 2 GBW 4-(2-METHYL-1-OXIDANYLIDENE-2,7-NAPHTHYRIDIN-4-YL) HETNAM 3 GBW PHENYL]METHYL]PIPERAZIN-1- HETNAM 4 GBW YL]ETHOXY]ETHOXY]ETHANOYLAMINO]-3,3-DIMETHYL- HETNAM 5 GBW BUTANOYL]-~{N}-[[4-(4-METHYL-1,3-THIAZOL-5-YL) HETNAM 6 GBW PHENYL]METHYL]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE FORMUL 3 GBW 2(C50 H64 N8 O9 S) FORMUL 5 HOH *68(H2 O) HELIX 1 AA1 THR A 23 ARG A 38 1 16 HELIX 2 AA2 GLY A 56 ILE A 61 1 6 HELIX 3 AA3 ASP A 66 ALA A 76 1 11 HELIX 4 AA4 SER A 81 ASN A 100 1 20 HELIX 5 AA5 THR A 104 MET A 121 1 18 HELIX 6 AA6 SER A 122 MET A 133 1 12 HELIX 7 AA7 THR B 23 ARG B 38 1 16 HELIX 8 AA8 GLY B 56 ILE B 61 1 6 HELIX 9 AA9 ASP B 66 ALA B 76 1 11 HELIX 10 AB1 SER B 81 ASN B 100 1 20 HELIX 11 AB2 THR B 104 MET B 121 1 18 HELIX 12 AB3 SER B 122 MET B 133 1 12 SITE 1 AC1 16 HIS A 42 GLY A 43 PHE A 44 PHE A 45 SITE 2 AC1 16 PHE A 47 VAL A 49 ILE A 53 ALA A 54 SITE 3 AC1 16 TYR A 99 ASN A 100 TYR A 106 HOH A 310 SITE 4 AC1 16 LYS B 90 ASP B 94 MET B 97 THR B 98 SITE 1 AC2 15 LYS A 90 MET A 97 HIS B 42 GLY B 43 SITE 2 AC2 15 PHE B 44 PHE B 45 PRO B 48 VAL B 49 SITE 3 AC2 15 ILE B 53 ALA B 54 TYR B 99 ASN B 100 SITE 4 AC2 15 TYR B 106 HOH B 305 HOH B 306 CRYST1 38.840 59.820 60.340 90.00 108.75 90.00 P 1 21 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 0.025747 0.000000 0.008740 0.00000 SCALE2 0.000000 0.016717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017502 0.00000