HEADER TRANSFERASE 30-JUN-11 3ZSO TITLE SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE TITLE 2 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CORE CATALYTIC DOMAIN, RESIDUES 56-212; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: INHIBITOR BOUND TO THE LEDGF SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 12721; SOURCE 4 STRAIN: TYPE 1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS TRANSFERASE, AIDS EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.NEWMAN,D.I.RHODES,J.J.DEADMAN,N.VANDERGRAAFF,G.LE, AUTHOR 2 E.D.JONES,J.A.SMITH,J.A.V.COATES,N.THIENTHONG,O.DOLEZAL,J.H.RYAN, AUTHOR 3 G.P.SAVAGE,C.L.FRANCIS REVDAT 5 20-DEC-23 3ZSO 1 REMARK REVDAT 4 06-FEB-19 3ZSO 1 REMARK REVDAT 3 30-JAN-19 3ZSO 1 REMARK REVDAT 2 01-AUG-12 3ZSO 1 AUTHOR JRNL REVDAT 1 11-JUL-12 3ZSO 0 JRNL AUTH T.S.PEAT,D.I.RHODES,N.VANDEGRAAFF,G.LE,J.A.SMITH,L.J.CLARK, JRNL AUTH 2 E.D.JONES,J.A.V.COATES,N.THIENTHONG,J.NEWMAN,O.DOLEZAL, JRNL AUTH 3 R.MULDER,J.H.RYAN,G.P.SAVAGE,C.L.FRANCIS,J.J.DEADMAN JRNL TITL SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS INTEGRASE IDENTIFIED BY FRAGMENT JRNL TITL 3 SCREENING AND STRUCTURE BASED DESIGN. JRNL REF PLOS ONE V. 7 40147 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22808106 JRNL DOI 10.1371/JOURNAL.PONE.0040147 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36193 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1930 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2617 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2332 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 146 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.08000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.984 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2776 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3816 ; 2.262 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 355 ; 6.192 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;33.590 ;25.478 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;13.882 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.289 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.172 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2222 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1641 ; 1.466 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2686 ; 2.493 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1135 ; 3.523 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1113 ; 5.075 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. RESIDUES 189-192 ARE DISORDERED. SULFATE IONS AND REMARK 3 OTHER HET ATOMS BESIDES THE KNOWN LIGAND ARE BEST GUESSES BASED REMARK 3 ON THE CRYSTALLIZATION AND CRYO CONDITIONS. REMARK 4 REMARK 4 3ZSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 61.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3NF7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, REMARK 280 PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 22.34233 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 44.68467 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: 5860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -168.6 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 56 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 139 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 185 TO HIS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 56 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 139 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 185 TO HIS 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 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 SER A 49 REMARK 465 HIS A 50 REMARK 465 HIS A 51 REMARK 465 HIS A 52 REMARK 465 HIS A 53 REMARK 465 HIS A 54 REMARK 465 HIS A 55 REMARK 465 SER A 56 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 GLY A 192 REMARK 465 LYS A 211 REMARK 465 GLU A 212 REMARK 465 MET B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 SER B 49 REMARK 465 HIS B 50 REMARK 465 HIS B 51 REMARK 465 HIS B 52 REMARK 465 HIS B 53 REMARK 465 HIS B 54 REMARK 465 HIS B 55 REMARK 465 SER B 56 REMARK 465 GLY B 189 REMARK 465 GLY B 190 REMARK 465 ILE B 191 REMARK 465 GLY B 192 REMARK 465 LYS B 211 REMARK 465 GLU B 212 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1 SO4 A 1214 NA NA A 1218 1.53 REMARK 500 O2 SO4 B 1214 NA NA B 1216 1.56 REMARK 500 NA NA B 1216 O HOH B 2025 1.58 REMARK 500 NA NA A 1218 O HOH A 2026 1.63 REMARK 500 OE1 GLU B 87 OXT ACY A 1215 1.88 REMARK 500 OE1 GLU A 87 OXT ACY A 1216 1.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 116 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 209 33.18 -77.00 REMARK 500 GLN B 209 32.87 -72.54 REMARK 500 REMARK 500 REMARK: NULL 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 NA B1216 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 B1214 S REMARK 620 2 HOH B2026 O 79.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1218 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O2N A 1219 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O2N B 1217 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZSQ RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT2 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT3 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT4 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSW RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 1HYZ RELATED DB: PDB REMARK 900 HIV INTEGRASE CORE DOMAIN COMPLEXED WITH A DERIVATIVE OFTETRAPHENYL REMARK 900 ARSONIUM. REMARK 900 RELATED ID: 1HYV RELATED DB: PDB REMARK 900 HIV INTEGRASE CORE DOMAIN COMPLEXED WITH TETRAPHENYLARSONIUM REMARK 900 RELATED ID: 3ZT1 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSX RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSZ RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT0 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSY RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSV RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSR RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN DBREF 3ZSO A 56 212 UNP Q76353 Q76353_9HIV1 56 212 DBREF 3ZSO B 56 212 UNP Q76353 Q76353_9HIV1 56 212 SEQADV 3ZSO MET A 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO GLY A 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER A 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER A 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS A 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER A 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZSO ASP A 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZSO HIS A 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQADV 3ZSO MET B 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO GLY B 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER B 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER B 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO HIS B 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZSO SER B 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZSO ASP B 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZSO HIS B 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQRES 1 A 167 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER PRO SEQRES 2 A 167 GLY ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS SEQRES 3 A 167 VAL ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE SEQRES 4 A 167 GLU ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR SEQRES 5 A 167 ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL SEQRES 6 A 167 LYS THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER SEQRES 7 A 167 THR THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS SEQRES 8 A 167 GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SER GLN GLY SEQRES 9 A 167 VAL ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE SEQRES 10 A 167 GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA SEQRES 11 A 167 VAL GLN MET ALA VAL PHE ILE HIS ASN HIS LYS ARG LYS SEQRES 12 A 167 GLY GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL SEQRES 13 A 167 ASP ILE ILE ALA THR ASP ILE GLN THR LYS GLU SEQRES 1 B 167 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER PRO SEQRES 2 B 167 GLY ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS SEQRES 3 B 167 VAL ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE SEQRES 4 B 167 GLU ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR SEQRES 5 B 167 ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL SEQRES 6 B 167 LYS THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER SEQRES 7 B 167 THR THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS SEQRES 8 B 167 GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SER GLN GLY SEQRES 9 B 167 VAL ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE SEQRES 10 B 167 GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA SEQRES 11 B 167 VAL GLN MET ALA VAL PHE ILE HIS ASN HIS LYS ARG LYS SEQRES 12 B 167 GLY GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL SEQRES 13 B 167 ASP ILE ILE ALA THR ASP ILE GLN THR LYS GLU HET SO4 A1211 5 HET SO4 A1212 5 HET SO4 A1213 5 HET SO4 A1214 5 HET ACY A1215 4 HET ACY A1216 4 HET ACY A1217 4 HET NA A1218 1 HET O2N A1219 44 HET SO4 B1211 5 HET SO4 B1212 5 HET SO4 B1213 5 HET SO4 B1214 5 HET ACY B1215 4 HET NA B1216 1 HET O2N B1217 44 HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETNAM NA SODIUM ION HETNAM O2N 5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL) HETNAM 2 O2N (PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4- HETNAM 3 O2N CARBOXYLIC ACID FORMUL 3 SO4 8(O4 S 2-) FORMUL 7 ACY 4(C2 H4 O2) FORMUL 10 NA 2(NA 1+) FORMUL 11 O2N 2(C35 H34 N2 O7) FORMUL 19 HOH *166(H2 O) HELIX 1 1 THR A 93 TRP A 108 1 16 HELIX 2 2 ASN A 117 SER A 123 1 7 HELIX 3 3 SER A 123 GLY A 134 1 12 HELIX 4 4 PRO A 145 ARG A 166 1 22 HELIX 5 5 ASP A 167 ALA A 169 5 3 HELIX 6 6 HIS A 171 LYS A 186 1 16 HELIX 7 7 SER A 195 GLN A 209 1 15 HELIX 8 8 THR B 93 TRP B 108 1 16 HELIX 9 9 ASN B 117 SER B 123 1 7 HELIX 10 10 SER B 123 GLY B 134 1 12 HELIX 11 11 PRO B 145 ARG B 166 1 22 HELIX 12 12 ASP B 167 ALA B 169 5 3 HELIX 13 13 HIS B 171 LYS B 186 1 16 HELIX 14 14 SER B 195 GLN B 209 1 15 SHEET 1 AA 5 ILE A 84 ILE A 89 0 SHEET 2 AA 5 LYS A 71 HIS A 78 -1 O VAL A 72 N ILE A 89 SHEET 3 AA 5 ILE A 60 LEU A 68 -1 O GLN A 62 N VAL A 77 SHEET 4 AA 5 THR A 112 HIS A 114 1 O THR A 112 N TRP A 61 SHEET 5 AA 5 LYS A 136 GLU A 138 1 O LYS A 136 N VAL A 113 SHEET 1 BA 5 ILE B 84 ILE B 89 0 SHEET 2 BA 5 LYS B 71 HIS B 78 -1 O VAL B 72 N ILE B 89 SHEET 3 BA 5 ILE B 60 LEU B 68 -1 O GLN B 62 N VAL B 77 SHEET 4 BA 5 THR B 112 HIS B 114 1 O THR B 112 N TRP B 61 SHEET 5 BA 5 LYS B 136 GLU B 138 1 O LYS B 136 N VAL B 113 LINK S SO4 A1214 NA NA A1218 1555 1555 2.84 LINK S SO4 B1214 NA NA B1216 1555 1555 2.95 LINK NA NA B1216 O HOH B2026 1555 1555 3.08 SITE 1 AC1 6 THR B 66 HIS B 67 LYS B 111 LYS B 136 SITE 2 AC1 6 LYS B 159 HOH B2048 SITE 1 AC2 6 THR A 66 HIS A 67 LYS A 111 LYS A 136 SITE 2 AC2 6 LYS A 159 HOH A2059 SITE 1 AC3 5 LYS B 71 HIS B 171 LEU B 172 HOH B2011 SITE 2 AC3 5 HOH B2060 SITE 1 AC4 6 LYS A 71 HIS A 171 LEU A 172 HOH A2009 SITE 2 AC4 6 HOH A2067 HOH A2070 SITE 1 AC5 7 GLU A 85 ALA A 86 GLU A 87 PHE A 100 SITE 2 AC5 7 LYS A 103 ARG B 107 SO4 B1213 SITE 1 AC6 7 ARG A 107 SO4 A1213 GLU B 85 ALA B 86 SITE 2 AC6 7 GLU B 87 PHE B 100 LYS B 103 SITE 1 AC7 8 GLY A 94 SER A 123 THR A 124 THR A 125 SITE 2 AC7 8 NA A1218 HOH A2026 HOH A2050 LYS B 186 SITE 1 AC8 7 GLY B 94 SER B 123 THR B 124 THR B 125 SITE 2 AC8 7 NA B1216 HOH B2025 HOH B2043 SITE 1 AC9 7 TYR A 99 LYS A 103 ACY A1216 HOH A2033 SITE 2 AC9 7 HOH A2088 GLU B 87 HOH B2061 SITE 1 BC1 7 GLU A 87 ACY A1215 HOH A2016 HOH A2017 SITE 2 BC1 7 HOH A2073 TYR B 99 LYS B 103 SITE 1 BC2 9 ALA A 105 GLY A 106 ARG A 107 TRP A 108 SITE 2 BC2 9 PRO A 109 ASN B 184 HIS B 185 GLY B 197 SITE 3 BC2 9 HOH B2071 SITE 1 BC3 8 ASN A 184 HIS A 185 GLY A 197 HOH A2082 SITE 2 BC3 8 GLY B 106 ARG B 107 TRP B 108 PRO B 109 SITE 1 BC4 3 SO4 B1214 HOH B2025 HOH B2026 SITE 1 BC5 2 SO4 A1214 HOH A2026 SITE 1 BC6 17 ASP A 167 GLN A 168 ALA A 169 GLU A 170 SITE 2 BC6 17 HIS A 171 THR A 174 HOH A2075 HOH A2089 SITE 3 BC6 17 GLN B 95 ALA B 98 TYR B 99 PHE B 121 SITE 4 BC6 17 THR B 125 ALA B 128 ALA B 129 TRP B 131 SITE 5 BC6 17 ASP B 139 SITE 1 BC7 19 GLN A 95 ALA A 98 TYR A 99 LEU A 102 SITE 2 BC7 19 PHE A 121 THR A 125 ALA A 128 ALA A 129 SITE 3 BC7 19 TRP A 131 ASP A 139 ILE A 141 ASP B 167 SITE 4 BC7 19 GLN B 168 ALA B 169 GLU B 170 HIS B 171 SITE 5 BC7 19 THR B 174 HOH B2063 HOH B2076 CRYST1 71.063 71.063 67.027 90.00 90.00 120.00 P 31 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 0.014072 0.008124 0.000000 0.00000 SCALE2 0.000000 0.016249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014919 0.00000