HEADER CYTOKINE 01-JUN-20 6X86 TITLE CRYSTAL STRUCTURE OF TNFALPHA WITH INDOLINONE COMPOUND 11 CAVEAT 6X86 SER E 86 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: CACHECTIN,TNF-ALPHA,TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY COMPND 5 MEMBER 2,TNF-A; 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: TNF, TNFA, TNFSF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRIMER, INHIBITOR COMPLEX, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.LONGENECKER,V.S.STOLL REVDAT 4 16-OCT-24 6X86 1 REMARK REVDAT 3 18-OCT-23 6X86 1 REMARK REVDAT 2 27-JAN-21 6X86 1 JRNL REVDAT 1 13-JAN-21 6X86 0 JRNL AUTH J.D.DIETRICH,K.L.LONGENECKER,N.S.WILSON,C.GOESS,S.C.PANCHAL, JRNL AUTH 2 S.L.SWANN,A.M.PETROS,A.D.HOBSON,D.IHLE,D.SONG,P.RICHARDSON, JRNL AUTH 3 K.M.COMESS,P.B.COX,A.DOMBROWSKI,K.SARRIS, JRNL AUTH 4 D.L.DONNELLY-ROBERTS,D.B.DUIGNAN,A.GOMTSYAN,P.JUNG, JRNL AUTH 5 A.C.KRUEGER,S.MATHIEU,A.MCCLURE,V.S.STOLL,J.WETTER, JRNL AUTH 6 J.A.MANKOVICH,P.J.HAJDUK,A.VASUDEVAN,R.H.STOFFEL,C.SUN JRNL TITL DEVELOPMENT OF ORALLY EFFICACIOUS ALLOSTERIC INHIBITORS OF JRNL TITL 2 TNF ALPHA VIA FRAGMENT-BASED DRUG DESIGN. JRNL REF J.MED.CHEM. V. 64 417 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33378180 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01280 REMARK 2 REMARK 2 RESOLUTION. 2.93 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) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 124.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18536 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 932 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 : 46 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.93 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.95 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 403 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2600 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 378 REMARK 3 BIN R VALUE (WORKING SET) : 0.2578 REMARK 3 BIN FREE R VALUE : 0.2944 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 25 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 : 6598 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.87810 REMARK 3 B22 (A**2) : -33.46110 REMARK 3 B33 (A**2) : 23.58300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 14.35060 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.360 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.416 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6832 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9309 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2303 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1200 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6832 ; 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 : 854 ; 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 : 7545 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.23 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.21 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.68 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 6X86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978720 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20171218 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18536 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 REMARK 200 RESOLUTION RANGE LOW (A) : 125.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1TNF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8000, 0.2M MAGNESIUM ACETATE, REMARK 280 0.05M SODIUM CACADYLATE, PH 6.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 124.84900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.35600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 124.84900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.35600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 0 REMARK 465 VAL A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 MET B 0 REMARK 465 VAL B 1 REMARK 465 ARG B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 ARG B 6 REMARK 465 THR B 7 REMARK 465 PRO B 8 REMARK 465 SER B 9 REMARK 465 ARG B 32 REMARK 465 ALA B 33 REMARK 465 ASN B 34 REMARK 465 ALA B 35 REMARK 465 LEU B 36 REMARK 465 LEU B 37 REMARK 465 ALA B 38 REMARK 465 ASN B 39 REMARK 465 ARG B 103 REMARK 465 GLU B 104 REMARK 465 THR B 105 REMARK 465 PRO B 106 REMARK 465 GLU B 107 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 GLU B 110 REMARK 465 ALA B 111 REMARK 465 MET C 0 REMARK 465 VAL C 1 REMARK 465 ARG C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 SER C 5 REMARK 465 ARG C 6 REMARK 465 GLN C 88 REMARK 465 THR C 89 REMARK 465 THR C 105 REMARK 465 PRO C 106 REMARK 465 GLU C 107 REMARK 465 GLY C 108 REMARK 465 ALA C 109 REMARK 465 GLU C 110 REMARK 465 ALA C 111 REMARK 465 MET D 0 REMARK 465 VAL D 1 REMARK 465 ARG D 2 REMARK 465 SER D 3 REMARK 465 SER D 4 REMARK 465 SER D 5 REMARK 465 ARG D 6 REMARK 465 TYR D 87 REMARK 465 GLN D 88 REMARK 465 THR D 89 REMARK 465 LYS D 90 REMARK 465 THR D 105 REMARK 465 PRO D 106 REMARK 465 GLU D 107 REMARK 465 GLY D 108 REMARK 465 ALA D 109 REMARK 465 GLU D 110 REMARK 465 ALA D 111 REMARK 465 LYS D 112 REMARK 465 MET E 0 REMARK 465 VAL E 1 REMARK 465 ARG E 2 REMARK 465 SER E 3 REMARK 465 SER E 4 REMARK 465 SER E 5 REMARK 465 ARG E 6 REMARK 465 THR E 7 REMARK 465 PRO E 8 REMARK 465 SER E 9 REMARK 465 TYR E 87 REMARK 465 GLN E 88 REMARK 465 THR E 89 REMARK 465 ARG E 103 REMARK 465 GLU E 104 REMARK 465 THR E 105 REMARK 465 PRO E 106 REMARK 465 GLU E 107 REMARK 465 GLY E 108 REMARK 465 ALA E 109 REMARK 465 GLU E 110 REMARK 465 ALA E 111 REMARK 465 MET F 0 REMARK 465 VAL F 1 REMARK 465 ARG F 2 REMARK 465 SER F 3 REMARK 465 SER F 4 REMARK 465 SER F 5 REMARK 465 ARG F 6 REMARK 465 THR F 105 REMARK 465 PRO F 106 REMARK 465 GLU F 107 REMARK 465 GLY F 108 REMARK 465 ALA F 109 REMARK 465 GLU F 110 REMARK 465 ALA F 111 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 GLN B 102 CA C O CB CG CD OE1 REMARK 470 GLN B 102 NE2 REMARK 470 VAL E 49 CG1 CG2 REMARK 470 GLN E 102 CA C O CB CG CD OE1 REMARK 470 GLN E 102 NE2 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 PRO A 70 -167.77 -75.74 REMARK 500 SER A 71 29.18 -70.24 REMARK 500 TYR A 87 5.94 58.77 REMARK 500 ARG A 138 79.74 -119.46 REMARK 500 ASN B 46 15.06 58.94 REMARK 500 SER B 86 -71.41 -63.79 REMARK 500 GLN B 88 65.18 -48.28 REMARK 500 SER B 147 172.13 -47.83 REMARK 500 GLN C 21 64.46 -114.09 REMARK 500 ASN C 34 22.53 83.63 REMARK 500 PRO C 70 68.25 -119.50 REMARK 500 SER C 71 -30.89 -158.52 REMARK 500 THR C 72 -157.50 -61.33 REMARK 500 ALA D 22 46.53 -85.30 REMARK 500 ASN D 30 42.11 -85.29 REMARK 500 ARG D 32 -57.24 -25.95 REMARK 500 ALA D 33 -84.71 -29.20 REMARK 500 ASN D 39 41.99 39.94 REMARK 500 SER D 60 133.85 -172.30 REMARK 500 SER D 95 146.01 -170.56 REMARK 500 ARG D 103 -153.18 179.08 REMARK 500 ARG E 31 -79.26 -73.52 REMARK 500 ARG E 32 166.05 -34.66 REMARK 500 ASP E 45 38.52 75.52 REMARK 500 GLU E 146 -7.36 65.37 REMARK 500 SER E 147 -168.78 -76.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTY B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTY F 201 DBREF 6X86 A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6X86 B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6X86 C 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6X86 D 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6X86 E 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6X86 F 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 6X86 MET A 0 UNP P01375 INITIATING METHIONINE SEQADV 6X86 MET B 0 UNP P01375 INITIATING METHIONINE SEQADV 6X86 MET C 0 UNP P01375 INITIATING METHIONINE SEQADV 6X86 MET D 0 UNP P01375 INITIATING METHIONINE SEQADV 6X86 MET E 0 UNP P01375 INITIATING METHIONINE SEQADV 6X86 MET F 0 UNP P01375 INITIATING METHIONINE SEQRES 1 A 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 A 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 A 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 A 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 A 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 A 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 A 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 A 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 A 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 A 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 A 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 A 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 A 158 ALA LEU SEQRES 1 B 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 B 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 B 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 B 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 B 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 B 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 B 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 B 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 B 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 B 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 B 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 B 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 B 158 ALA LEU SEQRES 1 C 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 C 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 C 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 C 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 C 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 C 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 C 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 C 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 C 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 C 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 C 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 C 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 C 158 ALA LEU SEQRES 1 D 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 D 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 D 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 D 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 D 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 D 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 D 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 D 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 D 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 D 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 D 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 D 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 D 158 ALA LEU SEQRES 1 E 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 E 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 E 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 E 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 E 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 E 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 E 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 E 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 E 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 E 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 E 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 E 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 E 158 ALA LEU SEQRES 1 F 158 MET VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 F 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 F 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 F 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 F 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 F 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 F 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 F 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 F 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 F 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 F 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 F 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 F 158 ALA LEU HET UTY B 901 38 HET UTY F 201 38 HETNAM UTY 3-[(6-{2-[(3R)-4-(HYDROXYACETYL)-3-METHYLPIPERAZIN-1- HETNAM 2 UTY YL]PYRIMIDIN-5-YL}-2,2-DIMETHYL-3-OXO-2,3-DIHYDRO-1H- HETNAM 3 UTY INDOL-1-YL)METHYL]PYRIDINE-2-CARBONITRILE FORMUL 7 UTY 2(C28 H29 N7 O3) FORMUL 9 HOH *60(H2 O) HELIX 1 AA1 VAL A 85 GLN A 88 5 4 HELIX 2 AA2 ARG A 138 LEU A 142 5 5 HELIX 3 AA3 ARG B 138 LEU B 142 5 5 HELIX 4 AA4 ARG C 138 LEU C 142 5 5 HELIX 5 AA5 ARG D 138 LEU D 142 5 5 HELIX 6 AA6 ARG E 138 LEU E 142 5 5 HELIX 7 AA7 ARG F 138 LEU F 142 5 5 SHEET 1 AA1 3 TRP A 28 LEU A 29 0 SHEET 2 AA1 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA1 3 LEU A 36 ALA A 38 -1 O LEU A 36 N HIS A 15 SHEET 1 AA2 5 TRP A 28 LEU A 29 0 SHEET 2 AA2 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA2 5 TYR A 151 ALA A 156 -1 O PHE A 152 N VAL A 16 SHEET 4 AA2 5 GLY A 54 GLN A 67 -1 N LEU A 57 O ILE A 155 SHEET 5 AA2 5 PRO A 113 LEU A 126 -1 O GLY A 122 N ILE A 58 SHEET 1 AA3 5 GLU A 42 ARG A 44 0 SHEET 2 AA3 5 GLN A 47 VAL A 49 -1 O VAL A 49 N GLU A 42 SHEET 3 AA3 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 AA3 5 LEU A 76 ALA A 84 -1 N THR A 79 O GLU A 135 SHEET 5 AA3 5 THR A 89 LYS A 98 -1 O VAL A 91 N ARG A 82 SHEET 1 AA4 5 TRP B 28 LEU B 29 0 SHEET 2 AA4 5 VAL B 13 ALA B 18 -1 N VAL B 17 O LEU B 29 SHEET 3 AA4 5 TYR B 151 ALA B 156 -1 O PHE B 152 N VAL B 16 SHEET 4 AA4 5 GLY B 54 GLN B 67 -1 N TYR B 59 O GLY B 153 SHEET 5 AA4 5 PRO B 113 LEU B 126 -1 O GLY B 122 N ILE B 58 SHEET 1 AA5 5 GLU B 42 ARG B 44 0 SHEET 2 AA5 5 GLN B 47 VAL B 49 -1 O VAL B 49 N GLU B 42 SHEET 3 AA5 5 ARG B 131 ILE B 136 -1 O LEU B 132 N LEU B 48 SHEET 4 AA5 5 LEU B 76 ILE B 83 -1 N THR B 79 O GLU B 135 SHEET 5 AA5 5 LYS B 90 LYS B 98 -1 O LEU B 94 N ILE B 80 SHEET 1 AA6 3 TRP C 28 LEU C 29 0 SHEET 2 AA6 3 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29 SHEET 3 AA6 3 LEU C 36 ALA C 38 -1 O LEU C 36 N HIS C 15 SHEET 1 AA7 5 TRP C 28 LEU C 29 0 SHEET 2 AA7 5 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29 SHEET 3 AA7 5 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16 SHEET 4 AA7 5 GLY C 54 GLY C 66 -1 N LEU C 57 O ILE C 155 SHEET 5 AA7 5 TRP C 114 LEU C 126 -1 O LEU C 120 N SER C 60 SHEET 1 AA8 5 GLU C 42 LEU C 43 0 SHEET 2 AA8 5 LEU C 48 VAL C 49 -1 O VAL C 49 N GLU C 42 SHEET 3 AA8 5 ARG C 131 ILE C 136 -1 O LEU C 132 N LEU C 48 SHEET 4 AA8 5 LEU C 76 ILE C 83 -1 N THR C 79 O GLU C 135 SHEET 5 AA8 5 VAL C 91 LYS C 98 -1 O LEU C 94 N ILE C 80 SHEET 1 AA9 3 TRP D 28 LEU D 29 0 SHEET 2 AA9 3 VAL D 13 ALA D 18 -1 N VAL D 17 O LEU D 29 SHEET 3 AA9 3 LEU D 36 LEU D 37 -1 O LEU D 36 N HIS D 15 SHEET 1 AB1 5 TRP D 28 LEU D 29 0 SHEET 2 AB1 5 VAL D 13 ALA D 18 -1 N VAL D 17 O LEU D 29 SHEET 3 AB1 5 TYR D 151 ALA D 156 -1 O PHE D 152 N VAL D 16 SHEET 4 AB1 5 GLY D 54 GLY D 66 -1 N LEU D 57 O ILE D 155 SHEET 5 AB1 5 TRP D 114 LEU D 126 -1 O GLY D 122 N ILE D 58 SHEET 1 AB2 5 GLU D 42 ARG D 44 0 SHEET 2 AB2 5 GLN D 47 VAL D 49 -1 O GLN D 47 N ARG D 44 SHEET 3 AB2 5 ARG D 131 ILE D 136 -1 O LEU D 132 N LEU D 48 SHEET 4 AB2 5 LEU D 76 ILE D 83 -1 N ILE D 83 O ARG D 131 SHEET 5 AB2 5 ASN D 92 LYS D 98 -1 O LYS D 98 N LEU D 76 SHEET 1 AB3 3 TRP E 28 LEU E 29 0 SHEET 2 AB3 3 VAL E 13 ALA E 18 -1 N VAL E 17 O LEU E 29 SHEET 3 AB3 3 LEU E 36 ALA E 38 -1 O ALA E 38 N VAL E 13 SHEET 1 AB4 5 TRP E 28 LEU E 29 0 SHEET 2 AB4 5 VAL E 13 ALA E 18 -1 N VAL E 17 O LEU E 29 SHEET 3 AB4 5 TYR E 151 ALA E 156 -1 O PHE E 152 N VAL E 16 SHEET 4 AB4 5 GLY E 54 LYS E 65 -1 N TYR E 59 O GLY E 153 SHEET 5 AB4 5 TYR E 115 LEU E 126 -1 O LEU E 126 N GLY E 54 SHEET 1 AB5 5 GLU E 42 LEU E 43 0 SHEET 2 AB5 5 LEU E 48 VAL E 49 -1 O VAL E 49 N GLU E 42 SHEET 3 AB5 5 ARG E 131 ILE E 136 -1 O LEU E 132 N LEU E 48 SHEET 4 AB5 5 LEU E 76 ILE E 83 -1 N THR E 79 O GLU E 135 SHEET 5 AB5 5 VAL E 91 LYS E 98 -1 O LEU E 94 N ILE E 80 SHEET 1 AB6 3 TRP F 28 LEU F 29 0 SHEET 2 AB6 3 VAL F 13 ALA F 18 -1 N VAL F 17 O LEU F 29 SHEET 3 AB6 3 LEU F 36 ALA F 38 -1 O LEU F 36 N HIS F 15 SHEET 1 AB7 5 TRP F 28 LEU F 29 0 SHEET 2 AB7 5 VAL F 13 ALA F 18 -1 N VAL F 17 O LEU F 29 SHEET 3 AB7 5 TYR F 151 ALA F 156 -1 O PHE F 152 N VAL F 16 SHEET 4 AB7 5 GLY F 54 GLN F 67 -1 N TYR F 59 O GLY F 153 SHEET 5 AB7 5 PRO F 113 LEU F 126 -1 O LEU F 120 N SER F 60 SHEET 1 AB8 5 GLU F 42 ARG F 44 0 SHEET 2 AB8 5 GLN F 47 VAL F 49 -1 O GLN F 47 N ARG F 44 SHEET 3 AB8 5 ARG F 131 ILE F 136 -1 O LEU F 132 N LEU F 48 SHEET 4 AB8 5 LEU F 76 ILE F 83 -1 N THR F 79 O GLU F 135 SHEET 5 AB8 5 LYS F 90 LYS F 98 -1 O LEU F 93 N ILE F 80 SSBOND 1 CYS A 69 CYS A 101 1555 1555 2.03 SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.03 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.04 SSBOND 4 CYS D 69 CYS D 101 1555 1555 2.03 SSBOND 5 CYS E 69 CYS E 101 1555 1555 2.04 SSBOND 6 CYS F 69 CYS F 101 1555 1555 2.04 CISPEP 1 PRO C 70 SER C 71 0 -1.52 CISPEP 2 SER E 147 GLY E 148 0 4.74 CISPEP 3 THR F 7 PRO F 8 0 1.31 SITE 1 AC1 18 LEU A 57 TYR A 119 ILE A 155 LEU A 157 SITE 2 AC1 18 LEU B 57 TYR B 59 SER B 60 LEU B 120 SITE 3 AC1 18 GLY B 121 GLY B 122 TYR B 151 ILE B 155 SITE 4 AC1 18 LYS C 11 LEU C 57 TYR C 119 GLY C 121 SITE 5 AC1 18 GLY C 122 LEU C 157 SITE 1 AC2 16 LYS D 11 LEU D 57 TYR D 119 ILE D 155 SITE 2 AC2 16 LEU E 57 TYR E 59 LEU E 120 GLY E 121 SITE 3 AC2 16 GLY E 122 TYR E 151 ILE E 155 LYS F 11 SITE 4 AC2 16 LEU F 57 TYR F 59 TYR F 119 GLY F 122 CRYST1 249.698 64.712 53.647 90.00 94.42 90.00 C 1 2 1 24 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 0.004005 0.000000 0.000310 0.00000 SCALE2 0.000000 0.015453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018696 0.00000