HEADER SIGNALING PROTEIN/INHIBITOR 27-SEP-17 6B4U TITLE CRYSTAL STRUCTURE OF MCL-1 IN COMPLEX WITH A BIM COMPETITIVE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN COMPND 6 EAT/MCL1,MCL1/EAT; COMPND 7 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: MCL1, BCL2L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MCL-1, SIGNALING PROTEIN-INHIBITOR COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.A.JUDGE,A.J.SOUERS REVDAT 2 13-MAR-24 6B4U 1 REMARK REVDAT 1 04-OCT-17 6B4U 0 JRNL AUTH M.BRUNCKO,L.WANG,G.S.SHEPPARD,D.C.PHILLIPS,S.K.TAHIR,J.XUE, JRNL AUTH 2 S.ERICKSON,S.FIDANZE,E.FRY,L.HASVOLD,G.J.JENKINS,S.JIN, JRNL AUTH 3 R.A.JUDGE,P.J.KOVAR,D.MADAR,P.NIMMER,C.PARK,A.M.PETROS, JRNL AUTH 4 S.H.ROSENBERG,M.L.SMITH,X.SONG,C.SUN,Z.F.TAO,X.WANG,Y.XIAO, JRNL AUTH 5 H.ZHANG,C.TSE,J.D.LEVERSON,S.W.ELMORE,A.J.SOUERS JRNL TITL STRUCTURE-GUIDED DESIGN OF A SERIES OF MCL-1 INHIBITORS WITH JRNL TITL 2 HIGH AFFINITY AND SELECTIVITY. JRNL REF J. MED. CHEM. V. 58 2180 2015 JRNL REFN ISSN 1520-4804 JRNL PMID 25679114 JRNL DOI 10.1021/JM501258M REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 12123 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 590 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.51 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2170 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2313 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2068 REMARK 3 BIN R VALUE (WORKING SET) : 0.2299 REMARK 3 BIN FREE R VALUE : 0.2597 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.01730 REMARK 3 B22 (A**2) : -7.77060 REMARK 3 B33 (A**2) : 4.75320 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.300 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.213 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.176 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.201 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.172 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1329 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1799 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 480 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 242 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1329 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 163 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1587 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.94 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.25 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.09 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6B4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 - 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18%(W/V)PEG 8000, 0.1M CHES PH 9.5, REMARK 280 4%(V/V)1,1,1,3,3,3 HEXAFLUOR-2-PROPANOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 44.67900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.67900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.17750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.29850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.17750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.29850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.67900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.17750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.29850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.67900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.17750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.29850 REMARK 290 SMTRY3 8 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 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 170 REMARK 465 GLY A 326 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CN7 A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VKC RELATED DB: PDB REMARK 900 SAME PROTEIN DIFFERENT LIGAND REMARK 900 RELATED ID: 6B4L RELATED DB: PDB REMARK 900 SAME PROTEIN DIFFERENT LIGAND DBREF 6B4U A 174 326 UNP Q07820 MCL1_HUMAN 174 326 SEQADV 6B4U GLY A 170 UNP Q07820 EXPRESSION TAG SEQADV 6B4U SER A 171 UNP Q07820 EXPRESSION TAG SEQADV 6B4U MET A 172 UNP Q07820 EXPRESSION TAG SEQADV 6B4U ASP A 173 UNP Q07820 EXPRESSION TAG SEQRES 1 A 157 GLY SER MET ASP LEU TYR ARG GLN SER LEU GLU ILE ILE SEQRES 2 A 157 SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP SEQRES 3 A 157 THR LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS SEQRES 4 A 157 ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN SEQRES 5 A 157 ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS SEQRES 6 A 157 LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER SEQRES 7 A 157 ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN SEQRES 8 A 157 TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE SEQRES 9 A 157 VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS SEQRES 10 A 157 ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL SEQRES 11 A 157 ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP SEQRES 12 A 157 ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU SEQRES 13 A 157 GLY HET CN7 A 401 41 HETNAM CN7 7-(2-METHYLPHENYL)-1-[2-(MORPHOLIN-4-YL)ETHYL]-3-{3- HETNAM 2 CN7 [(NAPHTHALEN-1-YL)OXY]PROPYL}-1H-INDOLE-2-CARBOXYLIC HETNAM 3 CN7 ACID FORMUL 2 CN7 C35 H36 N2 O4 FORMUL 3 HOH *108(H2 O) HELIX 1 AA1 SER A 171 GLY A 192 1 22 HELIX 2 AA2 SER A 202 HIS A 224 1 23 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 ASN A 239 SER A 255 1 17 HELIX 5 AA5 ASN A 260 ILE A 281 1 22 HELIX 6 AA6 GLN A 283 SER A 285 5 3 HELIX 7 AA7 CYS A 286 GLN A 309 1 24 HELIX 8 AA8 ARG A 310 PHE A 319 1 10 SITE 1 AC1 12 ALA A 227 ARG A 248 MET A 250 VAL A 253 SITE 2 AC1 12 ARG A 263 THR A 266 LEU A 267 PHE A 270 SITE 3 AC1 12 GLY A 271 VAL A 321 HOH A 532 HOH A 566 CRYST1 48.355 80.597 89.358 90.00 90.00 90.00 C 2 2 21 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 0.020680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011191 0.00000