HEADER SIGNALING PROTEIN/INHIBITOR 21-APR-17 5VKC 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, B; 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 EXPDTA X-RAY DIFFRACTION AUTHOR R.A.JUDGE,A.J.SOUERS REVDAT 3 13-MAR-24 5VKC 1 LINK REVDAT 2 23-AUG-17 5VKC 1 REMARK REVDAT 1 03-MAY-17 5VKC 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. 2.31 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 18180 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 933 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.45 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.34 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2891 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2160 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2750 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.88 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 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 : 2324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.57550 REMARK 3 B22 (A**2) : -3.57550 REMARK 3 B33 (A**2) : 7.15090 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) : 0.255 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.188 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.267 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.193 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 : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2526 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3426 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 898 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 58 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 418 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2526 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 5 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 304 ; 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 : 2908 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.08 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.34 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.45 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 5VKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18293 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7%(W/V) PEG 8000, 0.1M TRIS-HCL, PH REMARK 280 8.8, 0.2M ZINC ACETATE, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.93333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.46667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -229.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 170 REMARK 465 SER A 171 REMARK 465 ASP A 195 REMARK 465 THR A 196 REMARK 465 LYS A 197 REMARK 465 PRO A 198 REMARK 465 MET A 199 REMARK 465 GLY A 200 REMARK 465 ARG A 201 REMARK 465 ASP A 323 REMARK 465 LEU A 324 REMARK 465 GLU A 325 REMARK 465 GLY A 326 REMARK 465 GLY B 170 REMARK 465 SER B 171 REMARK 465 ASP B 195 REMARK 465 THR B 196 REMARK 465 LYS B 197 REMARK 465 PRO B 198 REMARK 465 MET B 199 REMARK 465 GLY B 200 REMARK 465 ARG B 201 REMARK 465 ASP B 323 REMARK 465 LEU B 324 REMARK 465 GLU B 325 REMARK 465 GLY B 326 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 173 -75.85 62.37 REMARK 500 ASP A 236 79.07 40.10 REMARK 500 ASP B 173 -75.66 59.66 REMARK 500 ASP B 236 78.93 40.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 556 DISTANCE = 11.98 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 224 NE2 REMARK 620 2 GLU A 288 OE1 65.7 REMARK 620 3 GLU A 288 OE2 66.9 4.2 REMARK 620 4 HOH A 506 O 99.1 105.9 101.7 REMARK 620 5 HOH A 529 O 109.7 50.5 51.9 122.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 407 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 241 OD2 REMARK 620 2 ASP B 242 OD1 39.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 406 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 242 OD1 REMARK 620 2 ASP B 241 OD2 65.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 252 NE2 REMARK 620 2 ASP A 256 OD2 117.0 REMARK 620 3 HOH A 537 O 110.7 105.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 405 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 252 ND1 REMARK 620 2 HOH A 515 O 102.3 REMARK 620 3 GLU B 292 OE2 27.3 82.7 REMARK 620 4 ASP B 296 OD2 29.3 81.2 2.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 292 OE2 REMARK 620 2 ASP A 296 OD2 102.6 REMARK 620 3 HIS B 252 ND1 58.4 44.9 REMARK 620 4 HOH B 532 O 62.4 40.5 5.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 408 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 320 NE2 REMARK 620 2 HOH A 540 O 102.3 REMARK 620 3 9EA B 401 N47 103.5 106.0 REMARK 620 4 HOH B 541 O 106.4 136.9 97.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 9EA A 401 N47 REMARK 620 2 HIS B 320 NE2 76.7 REMARK 620 3 HOH B 537 O 99.9 112.6 REMARK 620 4 HOH B 550 O 107.4 48.2 138.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 224 NE2 REMARK 620 2 GLU B 288 OE1 67.1 REMARK 620 3 GLU B 288 OE2 68.1 4.2 REMARK 620 4 HOH B 518 O 99.3 106.8 102.7 REMARK 620 5 HOH B 543 O 109.8 49.7 51.2 123.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 252 NE2 REMARK 620 2 ASP B 256 OD2 119.4 REMARK 620 3 HOH B 533 O 112.2 97.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9EA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9EA B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 404 DBREF 5VKC A 174 326 UNP Q07820 MCL1_HUMAN 174 326 DBREF 5VKC B 174 326 UNP Q07820 MCL1_HUMAN 174 326 SEQADV 5VKC GLY A 170 UNP Q07820 EXPRESSION TAG SEQADV 5VKC SER A 171 UNP Q07820 EXPRESSION TAG SEQADV 5VKC MET A 172 UNP Q07820 EXPRESSION TAG SEQADV 5VKC ASP A 173 UNP Q07820 EXPRESSION TAG SEQADV 5VKC GLY B 170 UNP Q07820 EXPRESSION TAG SEQADV 5VKC SER B 171 UNP Q07820 EXPRESSION TAG SEQADV 5VKC MET B 172 UNP Q07820 EXPRESSION TAG SEQADV 5VKC ASP B 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 SEQRES 1 B 157 GLY SER MET ASP LEU TYR ARG GLN SER LEU GLU ILE ILE SEQRES 2 B 157 SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP SEQRES 3 B 157 THR LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS SEQRES 4 B 157 ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN SEQRES 5 B 157 ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS SEQRES 6 B 157 LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER SEQRES 7 B 157 ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN SEQRES 8 B 157 TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE SEQRES 9 B 157 VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS SEQRES 10 B 157 ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL SEQRES 11 B 157 ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP SEQRES 12 B 157 ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU SEQRES 13 B 157 GLY HET 9EA A 401 57 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET ZN A 405 1 HET ZN A 406 1 HET ZN A 407 1 HET ZN A 408 1 HET 9EA B 401 57 HET ZN B 402 1 HET ZN B 403 1 HET ZN B 404 1 HETNAM 9EA 7-(3-{[4-(4-ACETYLPIPERAZIN-1-YL)PHENOXY]METHYL}-1,5- HETNAM 2 9EA DIMETHYL-1H-PYRAZOL-4-YL)-3-{3-[(NAPHTHALEN-1-YL) HETNAM 3 9EA OXY]PROPYL}-1-[(PYRIDIN-3-YL)METHYL]-1H-INDOLE-2- HETNAM 4 9EA CARBOXYLIC ACID HETNAM ZN ZINC ION FORMUL 3 9EA 2(C46 H46 N6 O5) FORMUL 4 ZN 10(ZN 2+) FORMUL 15 HOH *124(H2 O) HELIX 1 AA1 ASP A 173 GLY A 192 1 20 HELIX 2 AA2 GLY A 203 HIS A 224 1 22 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 ASN A 239 SER A 245 1 7 HELIX 5 AA5 SER A 245 ASP A 256 1 12 HELIX 6 AA6 ASN A 260 ILE A 281 1 22 HELIX 7 AA7 GLN A 283 SER A 285 5 3 HELIX 8 AA8 CYS A 286 GLN A 309 1 24 HELIX 9 AA9 ARG A 310 PHE A 319 1 10 HELIX 10 AB1 ASP B 173 GLY B 192 1 20 HELIX 11 AB2 GLY B 203 HIS B 224 1 22 HELIX 12 AB3 HIS B 224 ASP B 236 1 13 HELIX 13 AB4 ASN B 239 SER B 245 1 7 HELIX 14 AB5 SER B 245 ASP B 256 1 12 HELIX 15 AB6 ASN B 260 ILE B 281 1 22 HELIX 16 AB7 GLN B 283 SER B 285 5 3 HELIX 17 AB8 CYS B 286 GLN B 309 1 24 HELIX 18 AB9 ARG B 310 PHE B 319 1 10 LINK NE2 HIS A 224 ZN ZN A 402 1555 1555 2.11 LINK OD2 ASP A 241 ZN ZN A 407 1555 1555 2.48 LINK OD1 ASP A 242 ZN ZN A 406 1555 1555 2.22 LINK NE2 HIS A 252 ZN ZN A 404 1555 1555 2.11 LINK ND1 HIS A 252 ZN ZN A 405 1555 1555 1.92 LINK OD2 ASP A 256 ZN ZN A 404 1555 1555 2.08 LINK OE1 GLU A 288 ZN ZN A 402 1555 2564 2.44 LINK OE2 GLU A 288 ZN ZN A 402 1555 2564 2.04 LINK OE2 GLU A 292 ZN ZN B 403 1555 2564 2.09 LINK OD2 ASP A 296 ZN ZN B 403 1555 2564 2.02 LINK NE2 HIS A 320 ZN ZN A 408 1555 1555 2.07 LINK N47 9EA A 401 ZN ZN A 403 1555 1555 2.16 LINK ZN ZN A 402 O HOH A 506 1555 3455 2.05 LINK ZN ZN A 402 O HOH A 529 1555 3455 2.18 LINK ZN ZN A 403 NE2 HIS B 320 1565 1555 1.99 LINK ZN ZN A 403 O HOH B 537 1555 1545 1.89 LINK ZN ZN A 403 O HOH B 550 1555 1545 2.23 LINK ZN ZN A 404 O HOH A 537 1555 1555 2.07 LINK ZN ZN A 405 O HOH A 515 1555 1555 2.25 LINK ZN ZN A 405 OE2 GLU B 292 3455 1555 2.09 LINK ZN ZN A 405 OD2 ASP B 296 3455 1555 1.96 LINK ZN ZN A 406 OD2 ASP B 241 3455 1555 2.52 LINK ZN ZN A 407 OD1 ASP B 242 3455 1555 2.15 LINK ZN ZN A 408 O HOH A 540 1555 1555 2.26 LINK ZN ZN A 408 N47 9EA B 401 1555 1555 2.20 LINK ZN ZN A 408 O HOH B 541 1555 1555 1.89 LINK NE2 HIS B 224 ZN ZN B 402 1555 1555 2.13 LINK ND1 HIS B 252 ZN ZN B 403 1555 1555 1.92 LINK NE2 HIS B 252 ZN ZN B 404 1555 1555 2.11 LINK OD2 ASP B 256 ZN ZN B 404 1555 1555 2.03 LINK OE1 GLU B 288 ZN ZN B 402 1555 3355 2.46 LINK OE2 GLU B 288 ZN ZN B 402 1555 3355 2.07 LINK ZN ZN B 402 O HOH B 518 1555 1555 2.09 LINK ZN ZN B 402 O HOH B 543 1555 2574 2.17 LINK ZN ZN B 403 O HOH B 532 1555 1555 2.33 LINK ZN ZN B 404 O HOH B 533 1555 1555 1.89 SITE 1 AC1 15 HIS A 224 ALA A 227 MET A 250 VAL A 253 SITE 2 AC1 15 GLY A 262 ARG A 263 THR A 266 LEU A 267 SITE 3 AC1 15 PHE A 270 PHE A 319 ZN A 403 HOH A 506 SITE 4 AC1 15 HOH A 509 HOH A 512 HIS B 320 SITE 1 AC2 4 HIS A 224 GLU A 288 HOH A 506 HOH A 529 SITE 1 AC3 4 9EA A 401 HIS B 320 HOH B 537 HOH B 550 SITE 1 AC4 3 HIS A 252 ASP A 256 HOH A 537 SITE 1 AC5 5 ARG A 248 HIS A 252 HOH A 515 GLU B 292 SITE 2 AC5 5 ASP B 296 SITE 1 AC6 2 ASP A 242 ASP B 241 SITE 1 AC7 2 ASP A 241 ASP B 242 SITE 1 AC8 4 HIS A 320 HOH A 540 9EA B 401 HOH B 541 SITE 1 AC9 16 HIS A 320 ZN A 408 HIS B 224 ALA B 227 SITE 2 AC9 16 MET B 250 VAL B 253 GLY B 262 ARG B 263 SITE 3 AC9 16 THR B 266 LEU B 267 PHE B 270 PHE B 319 SITE 4 AC9 16 HOH B 502 HOH B 518 HOH B 538 HOH B 541 SITE 1 AD1 4 HIS B 224 GLU B 288 HOH B 518 HOH B 543 SITE 1 AD2 5 GLU A 292 ASP A 296 ARG B 248 HIS B 252 SITE 2 AD2 5 HOH B 532 SITE 1 AD3 4 GLU A 322 HIS B 252 ASP B 256 HOH B 533 CRYST1 63.920 63.920 91.400 90.00 90.00 120.00 P 32 6 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 0.015645 0.009032 0.000000 0.00000 SCALE2 0.000000 0.018065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010941 0.00000