HEADER OXIDOREDUCTASE 01-JUL-08 3DN5 TITLE ALDOSE REDUCTASE IN COMPLEX WITH NOVEL BIARYLIC INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDOSE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AR, ALDEHYDE REDUCTASE; COMPND 5 EC: 1.1.1.21; 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: ALR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TIM BARREL, NADPH BINDING SITE, ACETYLATION, CATARACT, CYTOPLASM, KEYWDS 2 NADP, OXIDOREDUCTASE, PHOSPHOPROTEIN, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR H.STEUBER,G.KLEBE REVDAT 3 01-NOV-23 3DN5 1 REMARK REVDAT 2 12-MAY-09 3DN5 1 JRNL REVDAT 1 07-APR-09 3DN5 0 JRNL AUTH M.EISENMANN,H.STEUBER,M.ZENTGRAF,M.ALTENKAMPER,R.ORTMANN, JRNL AUTH 2 J.PERRUCHON,G.KLEBE,M.SCHLITZER JRNL TITL STRUCTURE-BASED OPTIMIZATION OF ALDOSE REDUCTASE INHIBITORS JRNL TITL 2 ORIGINATING FROM VIRTUAL SCREENING JRNL REF CHEMMEDCHEM V. 4 809 2009 JRNL REFN ISSN 1860-7179 JRNL PMID 19301313 JRNL DOI 10.1002/CMDC.200800410 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.131 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2316 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 46659 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2517 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 356 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 2.100 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-06 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 : GRAPHITE 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : 0.03100 REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.09900 REMARK 200 R SYM FOR SHELL (I) : 0.09900 REMARK 200 FOR SHELL : 11.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 44.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 6000, 50MM AMMONIUM CITRATE PH REMARK 280 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 0 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 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TYR A 39 CB - CG - CD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 98 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 TYR A 209 CA - CB - CG ANGL. DEV. = 14.6 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 65 31.16 74.53 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 53N A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IKG RELATED DB: PDB REMARK 900 ALDOSE REDUCTASE COMPLEXED WITH NITROPHENYL-OXADIAZOL TYPE REMARK 900 INHIBITOR AT 1.43 A REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS BASED ON REFERENCE 2(AAA51714) IN THE REMARK 999 DATABASE, P63_P15121. DBREF 3DN5 A 0 315 UNP P15121 ALDR_HUMAN 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 53N A 600 19 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM 53N 3-[5-(3-NITROPHENYL)THIOPHEN-2-YL]PROPANOIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 53N C13 H11 N O4 S FORMUL 4 HOH *356(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 HIS A 240 1 11 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 GLY A 16 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 ILE A 109 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 37 GLY A 18 THR A 19 TRP A 20 LYS A 21 SITE 2 AC1 37 ASP A 43 TYR A 48 LYS A 77 HIS A 110 SITE 3 AC1 37 TRP A 111 SER A 159 ASN A 160 GLN A 183 SITE 4 AC1 37 TYR A 209 SER A 210 PRO A 211 LEU A 212 SITE 5 AC1 37 GLY A 213 SER A 214 PRO A 215 ASP A 216 SITE 6 AC1 37 ALA A 245 ILE A 260 PRO A 261 LYS A 262 SITE 7 AC1 37 SER A 263 VAL A 264 THR A 265 ARG A 268 SITE 8 AC1 37 GLU A 271 ASN A 272 53N A 600 HOH A1048 SITE 9 AC1 37 HOH A1049 HOH A1050 HOH A1071 HOH A1081 SITE 10 AC1 37 HOH A1155 SITE 1 AC2 14 TRP A 20 TYR A 48 HIS A 110 TRP A 111 SITE 2 AC2 14 THR A 113 PHE A 115 TRP A 219 CYS A 298 SITE 3 AC2 14 ALA A 299 LEU A 300 CYS A 303 TYR A 309 SITE 4 AC2 14 NAP A 500 HOH A1292 CRYST1 40.290 47.155 47.330 75.85 67.48 76.59 P 1 1 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 0.024820 -0.005918 -0.009408 0.00000 SCALE2 0.000000 0.021801 -0.003834 0.00000 SCALE3 0.000000 0.000000 0.023223 0.00000