HEADER CELL CYCLE/INHIBITOR 11-JAN-23 8I0M TITLE STRUCTURE OF CDK6 IN COMPLEX WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL DIVISION PROTEIN KINASE 6,SERINE/THREONINE-PROTEIN COMPND 5 KINASE PLSTIRE; COMPND 6 EC: 2.7.11.22; 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: CDK6, CDKN6; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS CDK6, INHIBITOR, COMPLEX, CELL CYCLE, CELL CYCLE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.JIANG,Y.YE,Y.HUANG REVDAT 1 24-JAN-24 8I0M 0 JRNL AUTH C.JIANG,Y.YE,Y.HUANG JRNL TITL STRUCTURE OF CDK6 IN COMPLEX WITH INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 7.1.010 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) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 7303 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 382 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2053 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.47000 REMARK 3 B22 (A**2) : 2.47000 REMARK 3 B33 (A**2) : -4.94000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.424 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.387 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.688 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: NULL REMARK 4 REMARK 4 8I0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-22 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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7680 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.772 REMARK 200 RESOLUTION RANGE LOW (A) : 27.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.16060 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M BIS-TRIS PH 7.0, 20% PEG 4,000, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 50.43500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.43500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.74000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.43500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.43500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.74000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 50.43500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 50.43500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.74000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 50.43500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 50.43500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.74000 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 GLY A 5 REMARK 465 LEU A 6 REMARK 465 CYS A 7 REMARK 465 ARG A 8 REMARK 465 ALA A 9 REMARK 465 ASP A 10 REMARK 465 ARG A 46 REMARK 465 VAL A 47 REMARK 465 GLN A 48 REMARK 465 THR A 49 REMARK 465 GLY A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 52 REMARK 465 GLY A 53 REMARK 465 MET A 54 REMARK 465 VAL A 85 REMARK 465 SER A 86 REMARK 465 ARG A 87 REMARK 465 THR A 88 REMARK 465 ASP A 89 REMARK 465 ARG A 90 REMARK 465 GLU A 91 REMARK 465 THR A 92 REMARK 465 LYS A 93 REMARK 465 ARG A 168 REMARK 465 ILE A 169 REMARK 465 TYR A 170 REMARK 465 SER A 171 REMARK 465 PHE A 172 REMARK 465 GLN A 173 REMARK 465 MET A 174 REMARK 465 ALA A 175 REMARK 465 LEU A 176 REMARK 465 THR A 177 REMARK 465 SER A 178 REMARK 465 VAL A 179 REMARK 465 VAL A 180 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 TYR A 24 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 LYS A 111 CG CD CE NZ 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 GLU A 21 -91.76 49.69 REMARK 500 GLU A 72 69.86 28.41 REMARK 500 ARG A 144 -19.79 79.68 REMARK 500 ASP A 145 48.28 -141.98 REMARK 500 ASP A 163 60.43 63.10 REMARK 500 ASP A 246 60.02 63.83 REMARK 500 SER A 258 -86.86 -87.83 REMARK 500 ALA A 259 77.03 154.30 REMARK 500 LEU A 281 37.15 -95.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 8I0M A 1 301 UNP Q00534 CDK6_HUMAN 1 301 SEQRES 1 A 301 MET GLU LYS ASP GLY LEU CYS ARG ALA ASP GLN GLN TYR SEQRES 2 A 301 GLU CYS VAL ALA GLU ILE GLY GLU GLY ALA TYR GLY LYS SEQRES 3 A 301 VAL PHE LYS ALA ARG ASP LEU LYS ASN GLY GLY ARG PHE SEQRES 4 A 301 VAL ALA LEU LYS ARG VAL ARG VAL GLN THR GLY GLU GLU SEQRES 5 A 301 GLY MET PRO LEU SER THR ILE ARG GLU VAL ALA VAL LEU SEQRES 6 A 301 ARG HIS LEU GLU THR PHE GLU HIS PRO ASN VAL VAL ARG SEQRES 7 A 301 LEU PHE ASP VAL CYS THR VAL SER ARG THR ASP ARG GLU SEQRES 8 A 301 THR LYS LEU THR LEU VAL PHE GLU HIS VAL ASP GLN ASP SEQRES 9 A 301 LEU THR THR TYR LEU ASP LYS VAL PRO GLU PRO GLY VAL SEQRES 10 A 301 PRO THR GLU THR ILE LYS ASP MET MET PHE GLN LEU LEU SEQRES 11 A 301 ARG GLY LEU ASP PHE LEU HIS SER HIS ARG VAL VAL HIS SEQRES 12 A 301 ARG ASP LEU LYS PRO GLN ASN ILE LEU VAL THR SER SER SEQRES 13 A 301 GLY GLN ILE LYS LEU ALA ASP PHE GLY LEU ALA ARG ILE SEQRES 14 A 301 TYR SER PHE GLN MET ALA LEU THR SER VAL VAL VAL THR SEQRES 15 A 301 LEU TRP TYR ARG ALA PRO GLU VAL LEU LEU GLN SER SER SEQRES 16 A 301 TYR ALA THR PRO VAL ASP LEU TRP SER VAL GLY CYS ILE SEQRES 17 A 301 PHE ALA GLU MET PHE ARG ARG LYS PRO LEU PHE ARG GLY SEQRES 18 A 301 SER SER ASP VAL ASP GLN LEU GLY LYS ILE LEU ASP VAL SEQRES 19 A 301 ILE GLY LEU PRO GLY GLU GLU ASP TRP PRO ARG ASP VAL SEQRES 20 A 301 ALA LEU PRO ARG GLN ALA PHE HIS SER LYS SER ALA GLN SEQRES 21 A 301 PRO ILE GLU LYS PHE VAL THR ASP ILE ASP GLU LEU GLY SEQRES 22 A 301 LYS ASP LEU LEU LEU LYS CYS LEU THR PHE ASN PRO ALA SEQRES 23 A 301 LYS ARG ILE SER ALA TYR SER ALA LEU SER HIS PRO TYR SEQRES 24 A 301 PHE GLN HET NJ6 A 401 27 HETNAM NJ6 2-[(4-AZANYLCYCLOHEXYL)AMINO]-7-CYCLOPENTYL-~{N},~{N}- HETNAM 2 NJ6 DIMETHYL-PYRROLO[2,3-D]PYRIMIDINE-6-CARBOXAMIDE FORMUL 2 NJ6 C20 H30 N6 O HELIX 1 AA1 LYS A 34 GLY A 36 5 3 HELIX 2 AA2 LEU A 56 THR A 70 1 15 HELIX 3 AA3 ASP A 104 LYS A 111 1 8 HELIX 4 AA4 PRO A 118 HIS A 139 1 22 HELIX 5 AA5 ALA A 187 LEU A 192 1 6 HELIX 6 AA6 THR A 198 ARG A 215 1 18 HELIX 7 AA7 SER A 223 GLY A 236 1 14 HELIX 8 AA8 GLY A 239 TRP A 243 5 5 HELIX 9 AA9 PRO A 250 PHE A 254 5 5 HELIX 10 AB1 PRO A 261 PHE A 265 5 5 HELIX 11 AB2 ASP A 270 LEU A 281 1 12 HELIX 12 AB3 SER A 290 LEU A 295 1 6 SHEET 1 AA1 5 TYR A 13 GLU A 21 0 SHEET 2 AA1 5 LYS A 26 ASP A 32 -1 O LYS A 29 N ALA A 17 SHEET 3 AA1 5 PHE A 39 ARG A 44 -1 O LEU A 42 N PHE A 28 SHEET 4 AA1 5 THR A 95 GLU A 99 -1 O PHE A 98 N ALA A 41 SHEET 5 AA1 5 LEU A 79 CYS A 83 -1 N ASP A 81 O VAL A 97 SHEET 1 AA2 2 ILE A 151 VAL A 153 0 SHEET 2 AA2 2 ILE A 159 LEU A 161 -1 O LYS A 160 N LEU A 152 CISPEP 1 GLU A 114 PRO A 115 0 16.77 CRYST1 100.870 100.870 59.480 90.00 90.00 90.00 I 4 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 0.009914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016812 0.00000