HEADER SIGNALING PROTEIN 24-APR-18 6GDM TITLE FRAGMENT-BASED DISCOVERY OF A HIGHLY POTENT, ORALLY BIOAVAILABLE TITLE 2 INHIBITOR WHICH MODULATES THE PHOSPHORYLATION AND CATALYTIC ACTIVITY TITLE 3 OF ERK1/2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOGEN-ACTIVATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAPK 1,ERT1,EXTRACELLULAR SIGNAL-REGULATED KINASE 2,ERK-2, COMPND 5 MAP KINASE ISOFORM P42,P42-MAPK,MITOGEN-ACTIVATED PROTEIN KINASE 2, COMPND 6 MAPK 2; COMPND 7 EC: 2.7.11.24; COMPND 8 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: MAPK1, ERK2, PRKM1, PRKM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ERK2 KINASE INHIBITOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.O'REILLY REVDAT 3 27-JUN-18 6GDM 1 JRNL REVDAT 2 13-JUN-18 6GDM 1 JRNL REVDAT 1 30-MAY-18 6GDM 0 JRNL AUTH T.D.HEIGHTMAN,V.BERDINI,H.BRAITHWAITE,I.M.BUCK,M.CASSIDY, JRNL AUTH 2 J.CASTRO,A.COURTIN,J.E.H.DAY,C.EAST,L.FAZAL,B.GRAHAM, JRNL AUTH 3 C.M.GRIFFITHS-JONES,J.F.LYONS,V.MARTINS,S.MUENCH,J.M.MUNCK, JRNL AUTH 4 D.NORTON,M.O'REILLY,N.PALMER,P.PATHURI,M.READER,D.C.REES, JRNL AUTH 5 S.J.RICH,C.RICHARDSON,H.SAINI,N.T.THOMPSON,N.G.WALLIS, JRNL AUTH 6 H.WALTON,N.E.WILSHER,A.J.WOOLFORD,M.COOKE,D.COUSIN,S.ONIONS, JRNL AUTH 7 J.SHANNON,J.WATTS,C.W.MURRAY JRNL TITL FRAGMENT-BASED DISCOVERY OF A POTENT, ORALLY BIOAVAILABLE JRNL TITL 2 INHIBITOR THAT MODULATES THE PHOSPHORYLATION AND CATALYTIC JRNL TITL 3 ACTIVITY OF ERK1/2. JRNL REF J. MED. CHEM. V. 61 4978 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29775310 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00421 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 28055 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1527 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1722 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 394 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.93000 REMARK 3 B22 (A**2) : 0.84000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.033 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2975 ; 0.010 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2693 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4032 ; 1.427 ; 1.768 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6323 ; 0.482 ; 1.728 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 6.551 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;37.082 ;21.125 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 503 ;14.637 ;16.461 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.151 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3258 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 542 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1384 ; 2.069 ; 4.073 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1384 ; 2.057 ; 4.072 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1591 ; 2.707 ; 4.811 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1592 ; 2.706 ; 4.813 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3386 ; 5.585 ;23.023 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3339 ; 5.542 ;22.570 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1017 3.5031 38.4725 REMARK 3 T TENSOR REMARK 3 T11: 0.0583 T22: 0.0440 REMARK 3 T33: 0.0184 T12: 0.0069 REMARK 3 T13: 0.0063 T23: -0.0249 REMARK 3 L TENSOR REMARK 3 L11: 2.0737 L22: 1.0172 REMARK 3 L33: 1.8234 L12: -0.5836 REMARK 3 L13: 0.7410 L23: -0.4600 REMARK 3 S TENSOR REMARK 3 S11: -0.0761 S12: -0.2647 S13: 0.1751 REMARK 3 S21: 0.2261 S22: 0.0677 S23: -0.0090 REMARK 3 S31: -0.1839 S32: -0.0947 S33: 0.0084 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6GDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30330 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 57.156 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35.0%W/V MPEG 2000, 0.2M (NH4)2SO4, REMARK 280 0.1M HEPES/NAOHPH=7.2, 0.02M MERCAPTOETHANOL, PH 7.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 35.34500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 ASP A 332 REMARK 465 MET A 333 REMARK 465 GLU A 334 REMARK 465 LEU A 335 REMARK 465 GLY A 357 REMARK 465 TYR A 358 REMARK 465 ARG A 359 REMARK 465 SER A 360 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 20 70.30 -108.47 REMARK 500 ASP A 149 42.42 -147.75 REMARK 500 ASP A 167 87.24 65.54 REMARK 500 ASP A 175 71.05 -152.67 REMARK 500 ASN A 201 20.44 -158.58 REMARK 500 LEU A 294 50.10 -97.63 REMARK 500 ASP A 318 91.69 -161.81 REMARK 500 PRO A 339 157.83 -49.28 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 893 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 894 DISTANCE = 7.52 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F3Z A 404 DBREF 6GDM A 1 360 UNP P28482 MK01_HUMAN 1 360 SEQADV 6GDM MET A -7 UNP P28482 INITIATING METHIONINE SEQADV 6GDM ALA A -6 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A -5 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A -4 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A -3 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A -2 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A -1 UNP P28482 EXPRESSION TAG SEQADV 6GDM HIS A 0 UNP P28482 EXPRESSION TAG SEQRES 1 A 368 MET ALA HIS HIS HIS HIS HIS HIS MET ALA ALA ALA ALA SEQRES 2 A 368 ALA ALA GLY ALA GLY PRO GLU MET VAL ARG GLY GLN VAL SEQRES 3 A 368 PHE ASP VAL GLY PRO ARG TYR THR ASN LEU SER TYR ILE SEQRES 4 A 368 GLY GLU GLY ALA TYR GLY MET VAL CYS SER ALA TYR ASP SEQRES 5 A 368 ASN VAL ASN LYS VAL ARG VAL ALA ILE LYS LYS ILE SER SEQRES 6 A 368 PRO PHE GLU HIS GLN THR TYR CME GLN ARG THR LEU ARG SEQRES 7 A 368 GLU ILE LYS ILE LEU LEU ARG PHE ARG HIS GLU ASN ILE SEQRES 8 A 368 ILE GLY ILE ASN ASP ILE ILE ARG ALA PRO THR ILE GLU SEQRES 9 A 368 GLN MET LYS ASP VAL TYR ILE VAL GLN ASP LEU MET GLU SEQRES 10 A 368 THR ASP LEU TYR LYS LEU LEU LYS THR GLN HIS LEU SER SEQRES 11 A 368 ASN ASP HIS ILE CYS TYR PHE LEU TYR GLN ILE LEU ARG SEQRES 12 A 368 GLY LEU LYS TYR ILE HIS SER ALA ASN VAL LEU HIS ARG SEQRES 13 A 368 ASP LEU LYS PRO SER ASN LEU LEU LEU ASN THR THR CME SEQRES 14 A 368 ASP LEU LYS ILE CME ASP PHE GLY LEU ALA ARG VAL ALA SEQRES 15 A 368 ASP PRO ASP HIS ASP HIS THR GLY PHE LEU THR GLU TYR SEQRES 16 A 368 VAL ALA THR ARG TRP TYR ARG ALA PRO GLU ILE MET LEU SEQRES 17 A 368 ASN SER LYS GLY TYR THR LYS SER ILE ASP ILE TRP SER SEQRES 18 A 368 VAL GLY CYS ILE LEU ALA GLU MET LEU SER ASN ARG PRO SEQRES 19 A 368 ILE PHE PRO GLY LYS HIS TYR LEU ASP GLN LEU ASN HIS SEQRES 20 A 368 ILE LEU GLY ILE LEU GLY SER PRO SER GLN GLU ASP LEU SEQRES 21 A 368 ASN CME ILE ILE ASN LEU LYS ALA ARG ASN TYR LEU LEU SEQRES 22 A 368 SER LEU PRO HIS LYS ASN LYS VAL PRO TRP ASN ARG LEU SEQRES 23 A 368 PHE PRO ASN ALA ASP SER LYS ALA LEU ASP LEU LEU ASP SEQRES 24 A 368 LYS MET LEU THR PHE ASN PRO HIS LYS ARG ILE GLU VAL SEQRES 25 A 368 GLU GLN ALA LEU ALA HIS PRO TYR LEU GLU GLN TYR TYR SEQRES 26 A 368 ASP PRO SER ASP GLU PRO ILE ALA GLU ALA PRO PHE LYS SEQRES 27 A 368 PHE ASP MET GLU LEU ASP ASP LEU PRO LYS GLU LYS LEU SEQRES 28 A 368 LYS GLU LEU ILE PHE GLU GLU THR ALA ARG PHE GLN PRO SEQRES 29 A 368 GLY TYR ARG SER MODRES 6GDM CME A 65 CYS MODIFIED RESIDUE MODRES 6GDM CME A 161 CYS MODIFIED RESIDUE MODRES 6GDM CME A 166 CYS MODIFIED RESIDUE MODRES 6GDM CME A 254 CYS MODIFIED RESIDUE HET CME A 65 10 HET CME A 161 10 HET CME A 166 10 HET CME A 254 10 HET SO4 A 401 5 HET DMS A 402 4 HET SO4 A 403 5 HET F3Z A 404 77 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM SO4 SULFATE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM F3Z (3~{R})-1-[2-OXIDANYLIDENE-2-[4-(4-PYRIMIDIN-2- HETNAM 2 F3Z YLPHENYL)PIPERAZIN-1-YL]ETHYL]-~{N}-(3-PYRIDIN-4-YL- HETNAM 3 F3Z 1~{H}-INDAZOL-5-YL)PYRROLIDINE-3-CARBOXAMIDE FORMUL 1 CME 4(C5 H11 N O3 S2) FORMUL 2 SO4 2(O4 S 2-) FORMUL 3 DMS C2 H6 O S FORMUL 5 F3Z C33 H33 N9 O2 FORMUL 6 HOH *394(H2 O) HELIX 1 AA1 HIS A 61 PHE A 78 1 18 HELIX 2 AA2 LEU A 112 GLN A 119 1 8 HELIX 3 AA3 SER A 122 ALA A 143 1 22 HELIX 4 AA4 LYS A 151 SER A 153 5 3 HELIX 5 AA5 ASP A 175 ASP A 179 5 5 HELIX 6 AA6 THR A 190 ARG A 194 5 5 HELIX 7 AA7 ALA A 195 ASN A 201 1 7 HELIX 8 AA8 LYS A 207 ASN A 224 1 18 HELIX 9 AA9 HIS A 232 GLY A 245 1 14 HELIX 10 AB1 SER A 248 CME A 254 1 7 HELIX 11 AB2 ASN A 257 LEU A 267 1 11 HELIX 12 AB3 PRO A 274 PHE A 279 1 6 HELIX 13 AB4 ASP A 283 LEU A 294 1 12 HELIX 14 AB5 GLU A 303 ALA A 309 1 7 HELIX 15 AB6 HIS A 310 GLU A 314 5 5 HELIX 16 AB7 ASP A 318 GLU A 322 5 5 HELIX 17 AB8 PRO A 339 ALA A 352 1 14 HELIX 18 AB9 ARG A 353 GLN A 355 5 3 SHEET 1 AA1 2 GLU A 12 VAL A 14 0 SHEET 2 AA1 2 GLN A 17 PHE A 19 -1 O PHE A 19 N GLU A 12 SHEET 1 AA2 5 TYR A 25 GLY A 34 0 SHEET 2 AA2 5 GLY A 37 ASP A 44 -1 O SER A 41 N SER A 29 SHEET 3 AA2 5 VAL A 49 ILE A 56 -1 O LYS A 55 N MET A 38 SHEET 4 AA2 5 VAL A 101 GLN A 105 -1 O GLN A 105 N ALA A 52 SHEET 5 AA2 5 ASP A 88 ILE A 90 -1 N ILE A 90 O TYR A 102 SHEET 1 AA3 3 THR A 110 ASP A 111 0 SHEET 2 AA3 3 LEU A 155 LEU A 157 -1 O LEU A 157 N THR A 110 SHEET 3 AA3 3 LEU A 163 ILE A 165 -1 O LYS A 164 N LEU A 156 SHEET 1 AA4 2 VAL A 145 LEU A 146 0 SHEET 2 AA4 2 ARG A 172 VAL A 173 -1 O ARG A 172 N LEU A 146 LINK C TYR A 64 N CME A 65 1555 1555 1.32 LINK C CME A 65 N GLN A 66 1555 1555 1.33 LINK C THR A 160 N CME A 161 1555 1555 1.32 LINK C CME A 161 N ASP A 162 1555 1555 1.33 LINK C ILE A 165 N CME A 166 1555 1555 1.33 LINK C CME A 166 N ASP A 167 1555 1555 1.32 LINK C ASN A 253 N CME A 254 1555 1555 1.33 LINK C CME A 254 N ILE A 255 1555 1555 1.34 CISPEP 1 GLY A 22 PRO A 23 0 1.70 SITE 1 AC1 7 ARG A 191 ARG A 194 TYR A 233 HOH A 525 SITE 2 AC1 7 HOH A 533 HOH A 710 HOH A 720 SITE 1 AC2 3 ASP A 124 HIS A 125 ILE A 256 SITE 1 AC3 4 ARG A 67 LEU A 170 ARG A 172 VAL A 188 SITE 1 AC4 22 ALA A 35 TYR A 36 ALA A 52 LYS A 54 SITE 2 AC4 22 ILE A 56 TYR A 64 ARG A 67 THR A 68 SITE 3 AC4 22 GLU A 71 GLN A 105 ASP A 106 LEU A 107 SITE 4 AC4 22 MET A 108 GLU A 109 LEU A 156 CME A 166 SITE 5 AC4 22 ASP A 167 HOH A 544 HOH A 564 HOH A 625 SITE 6 AC4 22 HOH A 690 HOH A 823 CRYST1 48.722 70.690 60.615 90.00 109.45 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 0.020525 0.000000 0.007248 0.00000 SCALE2 0.000000 0.014146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017496 0.00000