HEADER APOPTOSIS 21-DEC-22 8HTR TITLE CRYSTAL STRUCTURE OF BCL2 IN COMPLEX WITH S-9C COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,M.XU,Y.FENG,Y.LIU REVDAT 2 05-JUN-24 8HTR 1 JRNL REVDAT 1 15-MAY-24 8HTR 0 JRNL AUTH Y.GUO,H.XUE,N.HU,Y.LIU,H.SUN,D.YU,L.QIN,G.SHI,F.WANG,L.XIN, JRNL AUTH 2 W.SUN,F.ZHANG,X.SONG,S.LI,Q.WEI,Y.GUO,Y.LI,X.LIU,S.CHEN, JRNL AUTH 3 T.ZHANG,Y.WU,D.SU,Y.ZHU,A.XU,H.XU,S.YANG,Z.ZHENG,J.LIU, JRNL AUTH 4 X.YANG,X.YUAN,Y.HONG,X.SUN,Y.GUO,C.ZHOU,X.LIU,L.WANG,Z.WANG JRNL TITL DISCOVERY OF THE CLINICAL CANDIDATE SONROTOCLAX (BGB-11417), JRNL TITL 2 A HIGHLY POTENT AND SELECTIVE INHIBITOR FOR BOTH WT AND JRNL TITL 3 G101V MUTANT BCL-2. JRNL REF J.MED.CHEM. V. 67 7836 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 38695063 JRNL DOI 10.1021/ACS.JMEDCHEM.4C00027 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 17202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1782 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 31.0000 - 3.7600 0.97 1260 127 0.1834 0.2179 REMARK 3 2 3.7600 - 2.9900 0.98 1213 140 0.1827 0.2110 REMARK 3 3 2.9900 - 2.6100 0.98 1217 135 0.2049 0.2542 REMARK 3 4 2.6100 - 2.3700 0.99 1192 154 0.2061 0.2243 REMARK 3 5 2.3700 - 2.2000 0.99 1214 158 0.1905 0.2361 REMARK 3 6 2.2000 - 2.0700 0.97 1199 124 0.1962 0.2520 REMARK 3 7 2.0700 - 1.9700 0.99 1204 151 0.1957 0.2268 REMARK 3 8 1.9700 - 1.8800 0.99 1199 144 0.2008 0.2570 REMARK 3 9 1.8800 - 1.8100 0.99 1224 128 0.2059 0.2201 REMARK 3 10 1.8100 - 1.7500 0.99 1209 130 0.2167 0.3258 REMARK 3 11 1.7500 - 1.6900 0.98 1193 143 0.2231 0.2577 REMARK 3 12 1.6900 - 1.6400 0.90 1087 145 0.2589 0.2872 REMARK 3 13 1.6400 - 1.6000 0.82 1009 103 0.2706 0.3525 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) : 27.010 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 : 0.007 1269 REMARK 3 ANGLE : 0.873 1720 REMARK 3 CHIRALITY : 0.052 167 REMARK 3 PLANARITY : 0.011 217 REMARK 3 DIHEDRAL : 8.963 217 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 8HTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-18 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 32.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.68300 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 REMARK 200 STARTING MODEL: 5VAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5, 17% PEG 10000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 20.29850 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 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 -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 ALA A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 31 REMARK 465 ALA A 32 REMARK 465 GLY A 33 REMARK 465 ASP A 34 REMARK 465 ASP A 35 REMARK 465 VAL A 36 REMARK 465 GLU A 37 REMARK 465 GLU A 38 REMARK 465 ASN A 39 REMARK 465 ARG A 40 REMARK 465 THR A 41 REMARK 465 GLU A 42 REMARK 465 ALA A 43 REMARK 465 PRO A 44 REMARK 465 GLU A 45 REMARK 465 GLY A 46 REMARK 465 THR A 47 REMARK 465 GLU A 48 REMARK 465 SER A 205 REMARK 465 MET A 206 REMARK 465 ARG A 207 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 105 OG DBREF 8HTR A -4 207 PDB 8HTR 8HTR -4 207 SEQRES 1 A 171 GLY PRO LEU GLY SER MET ALA HIS ALA GLY ARG THR GLY SEQRES 2 A 171 TYR ASP ASN ARG GLU ILE VAL MET LYS TYR ILE HIS TYR SEQRES 3 A 171 LYS LEU SER GLN ARG GLY TYR GLU TRP ASP ALA GLY ASP SEQRES 4 A 171 ASP VAL GLU GLU ASN ARG THR GLU ALA PRO GLU GLY THR SEQRES 5 A 171 GLU SER GLU VAL VAL HIS LEU THR LEU ARG GLN ALA GLY SEQRES 6 A 171 ASP ASP PHE SER ARG ARG TYR ARG ARG ASP PHE ALA GLU SEQRES 7 A 171 MET SER SER GLN LEU HIS LEU THR PRO PHE THR ALA ARG SEQRES 8 A 171 GLY ARG PHE ALA THR VAL VAL GLU GLU LEU PHE ARG ASP SEQRES 9 A 171 GLY VAL ASN TRP GLY ARG ILE VAL ALA PHE PHE GLU PHE SEQRES 10 A 171 GLY GLY VAL MET CYS VAL GLU SER VAL ASN ARG GLU MET SEQRES 11 A 171 SER PRO LEU VAL ASP ASN ILE ALA LEU TRP MET THR GLU SEQRES 12 A 171 TYR LEU ASN ARG HIS LEU HIS THR TRP ILE GLN ASP ASN SEQRES 13 A 171 GLY GLY TRP ASP ALA PHE VAL GLU LEU TYR GLY PRO SER SEQRES 14 A 171 MET ARG HET MWH A 301 57 HETNAM MWH 4-[4-[(2~{S})-2-(2-CHLOROPHENYL)PYRROLIDIN-1- HETNAM 2 MWH YL]PHENYL]-~{N}-[3-NITRO-4-(OXAN-4-YLMETHYLAMINO) HETNAM 3 MWH PHENYL]SULFONYL-2-(1~{H}-PYRROLO[2,3-B]PYRIDIN-5- HETNAM 4 MWH YLOXY)BENZAMIDE FORMUL 2 MWH C42 H39 CL N6 O7 S FORMUL 3 HOH *60(H2 O) HELIX 1 AA1 ARG A 6 ARG A 26 1 21 HELIX 2 AA2 GLU A 50 TYR A 108 1 18 HELIX 3 AA3 TYR A 108 HIS A 120 1 13 HELIX 4 AA4 THR A 125 PHE A 138 1 14 HELIX 5 AA5 ASN A 143 ARG A 164 1 22 HELIX 6 AA6 PRO A 168 LEU A 185 1 18 HELIX 7 AA7 LEU A 185 ASN A 192 1 8 HELIX 8 AA8 GLY A 193 GLY A 203 1 11 CRYST1 31.902 40.597 53.808 90.00 103.66 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 0.031346 0.000000 0.007619 0.00000 SCALE2 0.000000 0.024632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019126 0.00000