HEADER OXIDOREDUCTASE 30-MAR-05 1Z89 TITLE HUMAN ALDOSE REDUCTASE COMPLEXED WITH NOVEL SULFONYL-PYRIDAZINONE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDOSE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.21; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS SULFONYL-PYRIDAZINONE, TIM-BARREL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.STEUBER,M.ZENTGRAF,A.PODJARNY,A.HEINE,G.KLEBE REVDAT 3 23-AUG-23 1Z89 1 REMARK REVDAT 2 24-FEB-09 1Z89 1 VERSN REVDAT 1 14-MAR-06 1Z89 0 JRNL AUTH H.STEUBER,M.ZENTGRAF,A.PODJARNY,A.HEINE,G.KLEBE JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF ALDOSE REDUCTASE JRNL TITL 2 COMPLEXED WITH THE NOVEL SULFONYL-PYRIDAZINONE INHIBITOR JRNL TITL 3 EXHIBITING AN ALTERNATIVE ACTIVE SITE ANCHORING GROUP. JRNL REF J.MOL.BIOL. V. 356 45 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16337231 JRNL DOI 10.1016/J.JMB.2005.10.067 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.163 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2735 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 53827 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.151 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 41679 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2525 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2933.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2511.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11897 REMARK 3 NUMBER OF RESTRAINTS : 10883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.057 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.063 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.028 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.059 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47200 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1EL3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM CITRATE, PEG 6000, PH 5, REMARK 280 VAPOR DIFFUSION, HANGING 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 33.45000 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 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 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 PHE A 115 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PHE A 121 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 HIS A 187 CG - ND1 - CE1 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR A 209 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 GLN A 283 CG - CD - OE1 ANGL. DEV. = 17.5 DEGREES REMARK 500 HIS A 306 CB - CG - CD2 ANGL. DEV. = 8.9 DEGREES REMARK 500 HIS A 306 CG - ND1 - CE1 ANGL. DEV. = 6.0 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 LYS A 21 3.77 83.18 REMARK 500 ARG A 293 18.92 -140.08 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 NAP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 62P A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z8A RELATED DB: PDB REMARK 900 HUMAN ALDOSE REDUCTASE COMPLEXED WITH NOVEL SULFONYL-PYRIDAZINONE REMARK 900 INHIBITOR AT 0.95 A RESOLUTION REMARK 900 RELATED ID: 1US0 RELATED DB: PDB REMARK 900 ALDOSE REDUCTASE COMPLEX AT 0.66 A RESOLUTION DBREF 1Z89 A 0 315 GB 178489 AAA51714 1 316 SEQRES 1 A 316 MET ALA SER ARG ILE LEU LEU ASN ASN GLY ALA LYS MET SEQRES 2 A 316 PRO ILE LEU GLY LEU GLY THR TRP LYS SER PRO PRO GLY SEQRES 3 A 316 GLN VAL THR GLU ALA VAL LYS VAL ALA ILE ASP VAL GLY SEQRES 4 A 316 TYR ARG HIS ILE ASP CYS ALA HIS VAL TYR GLN ASN GLU SEQRES 5 A 316 ASN GLU VAL GLY VAL ALA ILE GLN GLU LYS LEU ARG GLU SEQRES 6 A 316 GLN VAL VAL LYS ARG GLU GLU LEU PHE ILE VAL SER LYS SEQRES 7 A 316 LEU TRP CYS THR TYR HIS GLU LYS GLY LEU VAL LYS GLY SEQRES 8 A 316 ALA CYS GLN LYS THR LEU SER ASP LEU LYS LEU ASP TYR SEQRES 9 A 316 LEU ASP LEU TYR LEU ILE HIS TRP PRO THR GLY PHE LYS SEQRES 10 A 316 PRO GLY LYS GLU PHE PHE PRO LEU ASP GLU SER GLY ASN SEQRES 11 A 316 VAL VAL PRO SER ASP THR ASN ILE LEU ASP THR TRP ALA SEQRES 12 A 316 ALA MET GLU GLU LEU VAL ASP GLU GLY LEU VAL LYS ALA SEQRES 13 A 316 ILE GLY ILE SER ASN PHE ASN HIS LEU GLN VAL GLU MET SEQRES 14 A 316 ILE LEU ASN LYS PRO GLY LEU LYS TYR LYS PRO ALA VAL SEQRES 15 A 316 ASN GLN ILE GLU CYS HIS PRO TYR LEU THR GLN GLU LYS SEQRES 16 A 316 LEU ILE GLN TYR CYS GLN SER LYS GLY ILE VAL VAL THR SEQRES 17 A 316 ALA TYR SER PRO LEU GLY SER PRO ASP ARG PRO TRP ALA SEQRES 18 A 316 LYS PRO GLU ASP PRO SER LEU LEU GLU ASP PRO ARG ILE SEQRES 19 A 316 LYS ALA ILE ALA ALA LYS HIS ASN LYS THR THR ALA GLN SEQRES 20 A 316 VAL LEU ILE ARG PHE PRO MET GLN ARG ASN LEU VAL VAL SEQRES 21 A 316 ILE PRO LYS SER VAL THR PRO GLU ARG ILE ALA GLU ASN SEQRES 22 A 316 PHE LYS VAL PHE ASP PHE GLU LEU SER SER GLN ASP MET SEQRES 23 A 316 THR THR LEU LEU SER TYR ASN ARG ASN TRP ARG VAL CYS SEQRES 24 A 316 ALA LEU LEU SER CYS THR SER HIS LYS ASP TYR PRO PHE SEQRES 25 A 316 HIS GLU GLU PHE HET NAP A 500 48 HET 62P A 600 21 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM 62P 6-[(5-CHLORO-3-METHYL-1-BENZOFURAN-2-YL) HETNAM 2 62P SULFONYL]PYRIDAZIN-3(2H)-ONE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 62P C13 H9 CL N2 O4 S FORMUL 4 HOH *345(H2 O) HELIX 1 1 PRO A 23 GLY A 38 1 16 HELIX 2 2 ALA A 45 GLN A 49 5 5 HELIX 3 3 ASN A 50 GLU A 64 1 15 HELIX 4 4 LYS A 68 LEU A 72 5 5 HELIX 5 5 TRP A 79 HIS A 83 5 5 HELIX 6 6 GLU A 84 GLY A 86 5 3 HELIX 7 7 LEU A 87 LYS A 100 1 14 HELIX 8 8 ASN A 136 GLU A 150 1 15 HELIX 9 9 ASN A 162 ASN A 171 1 10 HELIX 10 10 GLN A 192 LYS A 202 1 11 HELIX 11 11 SER A 226 GLU A 229 5 4 HELIX 12 12 ASP A 230 ASN A 241 1 12 HELIX 13 13 THR A 243 GLN A 254 1 12 HELIX 14 14 THR A 265 LYS A 274 1 10 HELIX 15 15 SER A 281 SER A 290 1 10 HELIX 16 16 LEU A 300 THR A 304 5 5 SHEET 1 A 2 ARG A 3 LEU A 5 0 SHEET 2 A 2 LYS A 11 PRO A 13 -1 O MET A 12 N ILE A 4 SHEET 1 B 8 LEU A 17 GLY A 18 0 SHEET 2 B 8 HIS A 41 ASP A 43 1 O ASP A 43 N LEU A 17 SHEET 3 B 8 PHE A 73 LEU A 78 1 O VAL A 75 N ILE A 42 SHEET 4 B 8 LEU A 106 ILE A 109 1 O LEU A 108 N LEU A 78 SHEET 5 B 8 ILE A 156 SER A 159 1 O GLY A 157 N TYR A 107 SHEET 6 B 8 VAL A 181 GLU A 185 1 O VAL A 181 N ILE A 158 SHEET 7 B 8 VAL A 205 TYR A 209 1 O THR A 207 N ILE A 184 SHEET 8 B 8 VAL A 258 VAL A 259 1 O VAL A 258 N ALA A 208 SITE 1 AC1 35 GLY A 18 THR A 19 TRP A 20 LYS A 21 SITE 2 AC1 35 ASP A 43 TYR A 48 HIS A 110 SER A 159 SITE 3 AC1 35 ASN A 160 GLN A 183 TYR A 209 SER A 210 SITE 4 AC1 35 PRO A 211 LEU A 212 GLY A 213 SER A 214 SITE 5 AC1 35 PRO A 215 ASP A 216 ALA A 245 ILE A 260 SITE 6 AC1 35 PRO A 261 LYS A 262 SER A 263 VAL A 264 SITE 7 AC1 35 THR A 265 ARG A 268 GLU A 271 ASN A 272 SITE 8 AC1 35 62P A 600 HOH A1117 HOH A1131 HOH A1194 SITE 9 AC1 35 HOH A1197 HOH A1218 HOH A1303 SITE 1 AC2 14 TRP A 20 TYR A 48 TRP A 79 HIS A 110 SITE 2 AC2 14 TRP A 111 THR A 113 PHE A 122 TRP A 219 SITE 3 AC2 14 CYS A 298 ALA A 299 LEU A 300 TYR A 309 SITE 4 AC2 14 NAP A 500 HOH A1147 CRYST1 49.400 66.900 47.400 90.00 92.10 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 0.020227 0.000000 0.000756 0.00000 SCALE2 0.000000 0.014949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021118 0.00000