PDB Short entry for 4IEH HEADER APOPTOSIS/INHIBITOR 13-DEC-12 4IEH TITLE CRYSTAL STRUCTURE OF HUMAN BCL-2 IN COMPLEX WITH A SMALL MOLECULE TITLE 2 INHIBITOR TARGETING BCL-2 BH3 DOMAIN INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1 CHIMERA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: BCL2-L-1, APOPTOSIS REGULATOR BCL-X; COMPND 6 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: BCL2, BCL2L, BCL2L1, BCLX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-PROTEIN INTERACTION, ALPHA HELICAL, PRO-APOPTOSIS, CYTOCHROME KEYWDS 2 C RELEASE, CASPASE ACTIVATION, BIM, BAK, BAD, PUMA, APOPTOSIS- KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.XIE,R.KULATHILA REVDAT 4 28-FEB-24 4IEH 1 REMARK SEQADV REVDAT 3 26-JUL-17 4IEH 1 SOURCE REMARK REVDAT 2 24-SEP-14 4IEH 1 JRNL REVDAT 1 10-JUL-13 4IEH 0 JRNL AUTH B.B.TOURE,K.MILLER-MOSLIN,N.YUSUFF,L.PEREZ,M.DORE,C.JOUD, JRNL AUTH 2 W.MICHAEL,L.DIPIETRO,S.VAN DER PLAS,M.MCEWAN,F.LENOIR,M.HOE, JRNL AUTH 3 R.KARKI,C.SPRINGER,J.SULLIVAN,K.LEVINE,C.FIORILLA,X.XIE, JRNL AUTH 4 R.KULATHILA,K.HERLIHY,D.PORTER,M.VISSER JRNL TITL THE ROLE OF THE ACIDITY OF N-HETEROARYL SULFONAMIDES AS JRNL TITL 2 INHIBITORS OF BCL-2 FAMILY PROTEIN-PROTEIN INTERACTIONS. JRNL REF ACS MED CHEM LETT V. 4 186 2013 JRNL REFN ISSN 1948-5875 JRNL PMID 24900652 JRNL DOI 10.1021/ML300321D REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 798 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 45.7512 - 3.8154 0.99 2675 141 0.1840 0.2318 REMARK 3 2 3.8154 - 3.0285 1.00 2544 134 0.1579 0.1876 REMARK 3 3 3.0285 - 2.6458 1.00 2512 132 0.1740 0.1893 REMARK 3 4 2.6458 - 2.4039 1.00 2494 132 0.1750 0.2113 REMARK 3 5 2.4039 - 2.2316 1.00 2482 130 0.1803 0.2638 REMARK 3 6 2.2316 - 2.1000 1.00 2454 129 0.2018 0.2528 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 : 0.32 REMARK 3 B_SOL : 46.18 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.71990 REMARK 3 B22 (A**2) : -3.71990 REMARK 3 B33 (A**2) : 7.43980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 1261 REMARK 3 ANGLE : 0.980 1713 REMARK 3 CHIRALITY : 0.061 168 REMARK 3 PLANARITY : 0.006 216 REMARK 3 DIHEDRAL : 22.356 442 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 4IEH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) 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 : 15960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M SUCCINIC ACID, 0.25 M SODIUM REMARK 280 MALONATE, 12% PEG3350, 0.1 M TRIS-HCL, PH 8.6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 48.10250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.76450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.76450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.15375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.76450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.76450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.05125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.76450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.76450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.15375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.76450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.76450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.05125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.10250 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 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 -2 REMARK 465 SER A -1 REMARK 465 HIS 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 ARG A 6 REMARK 465 THR A 7 REMARK 465 GLY A 8 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 164 REMARK 465 MET A 165 REMARK 465 ARG A 166 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1E9 A 201 REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN IS A CHIMERA COMPRISING RESIDUES 1-34 OF BCL-2 (UNP P10415), REMARK 999 RESIDUES 29-44 OF BCL-X (UNP Q07817), AND RESIDUES 92-207 OF BCL-2 REMARK 999 (UNP P10415). DBREF 4IEH A 1 34 UNP P10415 BCL2_HUMAN 1 34 DBREF 4IEH A 35 50 UNP Q07817 B2CL1_HUMAN 29 44 DBREF 4IEH A 51 166 UNP P10415 BCL2_HUMAN 92 207 SEQADV 4IEH GLY A -2 UNP P10415 CLONING ARTIFACT SEQADV 4IEH SER A -1 UNP P10415 CLONING ARTIFACT SEQADV 4IEH HIS A 0 UNP P10415 CLONING ARTIFACT SEQRES 1 A 169 GLY SER HIS MET ALA HIS ALA GLY ARG THR GLY TYR ASP SEQRES 2 A 169 ASN ARG GLU ILE VAL MET LYS TYR ILE HIS TYR LYS LEU SEQRES 3 A 169 SER GLN ARG GLY TYR GLU TRP ASP ALA GLY ASP ASP VAL SEQRES 4 A 169 GLU GLU ASN ARG THR GLU ALA PRO GLU GLY THR GLU SER SEQRES 5 A 169 GLU VAL VAL HIS LEU THR LEU ARG GLN ALA GLY ASP ASP SEQRES 6 A 169 PHE SER ARG ARG TYR ARG ARG ASP PHE ALA GLU MET SER SEQRES 7 A 169 SER GLN LEU HIS LEU THR PRO PHE THR ALA ARG GLY ARG SEQRES 8 A 169 PHE ALA THR VAL VAL GLU GLU LEU PHE ARG ASP GLY VAL SEQRES 9 A 169 ASN TRP GLY ARG ILE VAL ALA PHE PHE GLU PHE GLY GLY SEQRES 10 A 169 VAL MET CYS VAL GLU SER VAL ASN ARG GLU MET SER PRO SEQRES 11 A 169 LEU VAL ASP ASN ILE ALA LEU TRP MET THR GLU TYR LEU SEQRES 12 A 169 ASN ARG HIS LEU HIS THR TRP ILE GLN ASP ASN GLY GLY SEQRES 13 A 169 TRP ASP ALA PHE VAL GLU LEU TYR GLY PRO SER MET ARG HET 1E9 A 201 59 HETNAM 1E9 N-(6-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1- HETNAM 2 1E9 YL}-1,1-DIOXIDO-1,2-BENZOTHIAZOL-3-YL)-4-{[(2R)-4- HETNAM 3 1E9 (DIMETHYLAMINO)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3- HETNAM 4 1E9 NITROBENZENESULFONAMIDE FORMUL 2 1E9 C42 H44 CL N7 O6 S3 FORMUL 3 HOH *184(H2 O) HELIX 1 1 ASP A 10 ARG A 26 1 17 HELIX 2 2 GLU A 50 TYR A 67 1 18 HELIX 3 3 TYR A 67 SER A 75 1 9 HELIX 4 4 SER A 76 LEU A 78 5 3 HELIX 5 5 THR A 84 PHE A 97 1 14 HELIX 6 6 ASN A 102 ARG A 123 1 22 HELIX 7 7 PRO A 127 LEU A 144 1 18 HELIX 8 8 LEU A 144 ASN A 151 1 8 HELIX 9 9 GLY A 152 GLY A 162 1 11 SITE 1 AC1 20 ALA A 59 ASP A 62 ARG A 66 TYR A 67 SITE 2 AC1 20 PHE A 71 MET A 74 GLY A 104 ARG A 105 SITE 3 AC1 20 VAL A 107 ALA A 108 GLU A 124 MET A 125 SITE 4 AC1 20 SER A 126 PHE A 157 TYR A 161 HOH A 319 SITE 5 AC1 20 HOH A 360 HOH A 366 HOH A 367 HOH A 436 CRYST1 73.529 73.529 96.205 90.00 90.00 90.00 P 43 21 2 8 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 0.013600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010394 0.00000