HEADER HYDROLASE/HYDROLASE INHIBITOR 26-OCT-09 3KEK TITLE CRYSTAL STRUCTURE OF HUMAN MMP-13 COMPLEXED WITH A (PYRIDIN-4-YL)-2H- TITLE 2 TETRAZOLE COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 104-270; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-13, MMP-13; COMPND 6 EC: 3.4.24.-; COMPND 7 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: MMP13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)/PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEMEX1 KEYWDS S1' INHIBITOR; SELECTIVE MMP-13 INHIBITOR; S1' SPECIFICITY, NO KEYWDS 2 CONTACT TO ZN, COLLAGEN DEGRADATION, DISEASE MUTATION, DISULFIDE KEYWDS 3 BOND, EXTRACELLULAR MATRIX, GLYCOPROTEIN, HYDROLASE, METAL-BINDING, KEYWDS 4 METALLOPROTEASE, PROTEASE, SECRETED, ZYMOGEN, HYDROLASE-HYDROLASE KEYWDS 5 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.-S.SHIEH,B.COLLINS,M.E.SCHNUTE REVDAT 3 21-FEB-24 3KEK 1 REMARK LINK REVDAT 2 01-NOV-17 3KEK 1 REMARK REVDAT 1 10-NOV-10 3KEK 0 JRNL AUTH M.E.SCHNUTE,P.M.O'BRIEN,J.NAHRA,M.MORRIS,W.HOWARD ROARK, JRNL AUTH 2 C.E.HANAU,P.G.RUMINSKI,J.A.SCHOLTEN,T.R.FLETCHER,B.C.HAMPER, JRNL AUTH 3 J.N.CARROLL,W.C.PATT,H.S.SHIEH,B.COLLINS,A.G.PAVLOVSKY, JRNL AUTH 4 K.E.PALMQUIST,K.W.ASTON,J.HITCHCOCK,M.D.ROGERS,J.MCDONALD, JRNL AUTH 5 A.R.JOHNSON,G.E.MUNIE,A.J.WITTWER,C.F.MAN,S.L.SETTLE, JRNL AUTH 6 O.NEMIROVSKIY,L.E.VICKERY,A.AGAWAL,R.D.DYER,T.SUNYER JRNL TITL DISCOVERY OF (PYRIDIN-4-YL)-2H-TETRAZOLE AS A NOVEL SCAFFOLD JRNL TITL 2 TO IDENTIFY HIGHLY SELECTIVE MATRIX METALLOPROTEINASE-13 JRNL TITL 3 INHIBITORS FOR THE TREATMENT OF OSTEOARTHRITIS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 576 2009 JRNL REFN ISSN 0960-894X JRNL PMID 20005097 JRNL DOI 10.1016/J.BMCL.2009.11.081 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 28595 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1502 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2023 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 576 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.24000 REMARK 3 B22 (A**2) : 1.29000 REMARK 3 B33 (A**2) : -0.05000 REMARK 3 B12 (A**2) : 0.00000 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): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.132 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2715 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1751 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3693 ; 1.136 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4262 ; 0.804 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 5.709 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;35.298 ;24.113 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 393 ;12.695 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;24.012 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3116 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 570 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 594 ; 0.183 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1732 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1316 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1207 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 336 ; 0.149 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 15 ; 0.132 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.127 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.212 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 39 ; 0.165 ; 0.200 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): 1634 ; 0.438 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 651 ; 0.082 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2574 ; 0.718 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1244 ; 1.085 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 1.575 ; 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 : 2 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 104 A 267 REMARK 3 ORIGIN FOR THE GROUP (A): 47.3017 29.8753 8.4104 REMARK 3 T TENSOR REMARK 3 T11: -0.1733 T22: -0.2064 REMARK 3 T33: -0.2111 T12: -0.0143 REMARK 3 T13: -0.0082 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 3.4716 L22: 1.2352 REMARK 3 L33: 1.8416 L12: 0.6937 REMARK 3 L13: -0.3193 L23: 0.5560 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: -0.0172 S13: 0.0437 REMARK 3 S21: -0.0128 S22: 0.0173 S23: 0.0698 REMARK 3 S31: 0.0099 S32: -0.1211 S33: -0.0257 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 104 B 267 REMARK 3 ORIGIN FOR THE GROUP (A): 77.2064 32.8402 34.2251 REMARK 3 T TENSOR REMARK 3 T11: -0.1677 T22: -0.1695 REMARK 3 T33: -0.1387 T12: 0.0290 REMARK 3 T13: -0.0161 T23: -0.0297 REMARK 3 L TENSOR REMARK 3 L11: 4.0484 L22: 1.2332 REMARK 3 L33: 1.7026 L12: -0.5561 REMARK 3 L13: -0.9754 L23: 0.2021 REMARK 3 S TENSOR REMARK 3 S11: 0.1155 S12: 0.1016 S13: 0.2183 REMARK 3 S21: -0.0789 S22: -0.0457 S23: -0.0568 REMARK 3 S31: -0.0700 S32: 0.0378 S33: -0.0699 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 REMARK 4 REMARK 4 3KEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000055893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.0 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 MICROMAX-002 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : CRYSTAL MONOCHROMATOR 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 : 30135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : 0.39000 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: FOURIER SYNTHESIS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 5.5 MG/ML MMP-13 WITH 200 UM REMARK 280 SURROGATE INHIBITOR IN 20MM TRIS PH 8.5 AND 5 MM CACL2. REMARK 280 RESERVOIR: 1.1-1.6M LI2SO4 IN 0.1M HEPES PH 7.4-8.2. DROP RATIO: REMARK 280 5UL PROTEIN + 1 UL RESERVOIR., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K, PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 60.42300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.42300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.87000 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 PRO A 268 REMARK 465 GLY A 269 REMARK 465 ASP A 270 REMARK 465 TYR B 104 REMARK 465 ASN B 105 REMARK 465 VAL B 106 REMARK 465 PHE B 107 REMARK 465 PRO B 108 REMARK 465 ARG B 109 REMARK 465 PRO B 268 REMARK 465 GLY B 269 REMARK 465 ASP B 270 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 TYR A 104 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 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 O HOH A 2090 O HOH A 2173 1.87 REMARK 500 O HOH B 2001 O HOH B 2247 2.00 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 170 -128.94 46.37 REMARK 500 SER A 182 -165.10 61.44 REMARK 500 ASN A 194 -113.94 59.75 REMARK 500 LYS B 170 -122.78 44.24 REMARK 500 TYR B 176 76.48 -117.83 REMARK 500 SER B 182 -165.04 62.24 REMARK 500 ASN B 194 -117.29 59.68 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 CA A 905 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 128 OD1 42.8 REMARK 620 3 ASP A 203 O 145.0 166.1 REMARK 620 4 ASP A 203 OD2 104.2 107.0 62.4 REMARK 620 5 GLU A 205 O 63.4 105.4 85.7 98.1 REMARK 620 6 HOH A2002 O 142.8 105.5 62.1 60.9 146.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 153.9 REMARK 620 3 GLY A 196 O 64.1 95.0 REMARK 620 4 ASP A 198 OD1 85.5 108.8 84.1 REMARK 620 5 HOH A2007 O 74.3 82.4 62.6 146.0 REMARK 620 6 HOH A2266 O 109.8 86.0 163.9 110.8 101.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 112.1 REMARK 620 3 HIS A 187 NE2 124.8 104.8 REMARK 620 4 HIS A 200 ND1 109.9 94.6 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 86.2 REMARK 620 3 SER A 182 O 84.6 87.6 REMARK 620 4 LEU A 184 O 88.6 173.9 95.2 REMARK 620 5 ASP A 202 OD2 94.6 87.5 175.1 89.7 REMARK 620 6 GLU A 205 OE2 173.0 93.8 88.4 91.8 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 103.1 REMARK 620 3 HIS A 232 NE2 117.7 92.1 REMARK 620 4 HOH A2159 O 115.2 102.4 119.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 143.1 REMARK 620 3 GLY B 196 O 57.0 90.7 REMARK 620 4 ASP B 198 OD1 80.3 113.8 80.0 REMARK 620 5 HOH B2026 O 70.2 78.6 60.2 139.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 112.0 REMARK 620 3 HIS B 187 NE2 108.8 116.3 REMARK 620 4 HIS B 200 ND1 110.8 91.8 116.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 94.1 REMARK 620 3 SER B 182 O 84.0 100.5 REMARK 620 4 LEU B 184 O 93.1 164.5 93.9 REMARK 620 5 ASP B 202 OD2 100.0 69.5 169.3 95.7 REMARK 620 6 GLU B 205 OE2 166.0 92.1 82.5 84.1 93.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 102.7 REMARK 620 3 HIS B 232 NE2 107.9 103.1 REMARK 620 4 HOH B2130 O 104.7 110.7 125.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3EK A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3EK B 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KEC RELATED DB: PDB REMARK 900 SAME SERIES OF MMP-13 S1' INHIBITORS REMARK 900 RELATED ID: 3KEJ RELATED DB: PDB REMARK 900 SAME SERIES OF MMP-13 S1' INHIBITORS DBREF 3KEK A 104 270 UNP P45452 MMP13_HUMAN 105 271 DBREF 3KEK B 104 270 UNP P45452 MMP13_HUMAN 105 271 SEQRES 1 A 167 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 167 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 167 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 167 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 167 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 167 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 167 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 167 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 167 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 167 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 167 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 167 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 167 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP SEQRES 1 B 167 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 B 167 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 B 167 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 B 167 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 B 167 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 B 167 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 167 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 B 167 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 B 167 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 B 167 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 B 167 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 B 167 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 B 167 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP HET ZN A 901 1 HET ZN A 902 1 HET CA A 903 1 HET CA A 904 1 HET CA A 905 1 HET 3EK A 801 33 HET ZN B 901 1 HET ZN B 902 1 HET CA B 903 1 HET CA B 904 1 HET CA B 905 1 HET 3EK B 801 33 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 3EK TRANS-4-[(3-{2-[(4-FLUOROBENZYL)CARBAMOYL]-6- HETNAM 2 3EK METHYLPYRIDIN-4-YL}-1H-1,2,4-TRIAZOL-1-YL) HETNAM 3 3EK METHYL]CYCLOHEXANECARBOXYLIC ACID HETSYN 3EK (1R,4R)-4-((3-(2((4-FLUOROBENZYL)CARBAMOYL)-6- HETSYN 2 3EK METHYLPYRIDIN-4-YL)-1H-1,2,4-TRIAZOL-1-YL) HETSYN 3 3EK METHYL]CYCLOHEXANECARBOXYLIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 3EK 2(C24 H26 F N5 O3) FORMUL 15 HOH *576(H2 O) HELIX 1 1 THR A 130 ASP A 147 1 18 HELIX 2 2 LEU A 216 GLY A 229 1 14 HELIX 3 3 PRO A 255 GLY A 267 1 13 HELIX 4 4 THR B 130 ASP B 147 1 18 HELIX 5 5 LEU B 216 GLY B 229 1 14 HELIX 6 6 PRO B 255 GLY B 267 1 13 SHEET 1 A 5 ASN A 152 LEU A 156 0 SHEET 2 A 5 ASN A 117 ILE A 122 1 N TYR A 120 O LEU A 156 SHEET 3 A 5 ILE A 163 GLY A 168 1 O ILE A 165 N ARG A 121 SHEET 4 A 5 ALA A 199 ASP A 202 1 O PHE A 201 N SER A 166 SHEET 5 A 5 ALA A 186 ALA A 188 -1 N HIS A 187 O HIS A 200 SHEET 1 B 2 TRP A 207 THR A 208 0 SHEET 2 B 2 TYR A 214 ASN A 215 1 O TYR A 214 N THR A 208 SHEET 1 C 5 ASN B 152 ARG B 155 0 SHEET 2 C 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152 SHEET 3 C 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 C 5 ALA B 199 ASP B 202 1 O ALA B 199 N MET B 164 SHEET 5 C 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 D 2 TRP B 207 THR B 208 0 SHEET 2 D 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208 LINK OD2 ASP A 128 CA CA A 905 1555 1555 2.81 LINK OD1 ASP A 128 CA CA A 905 1555 1555 3.13 LINK O ASP A 162 CA CA A 904 1555 1555 2.71 LINK NE2 HIS A 172 ZN ZN A 902 1555 1555 2.11 LINK OD2 ASP A 174 ZN ZN A 902 1555 1555 1.98 LINK OD1 ASP A 179 CA CA A 903 1555 1555 2.43 LINK O GLY A 180 CA CA A 903 1555 1555 2.25 LINK O SER A 182 CA CA A 903 1555 1555 2.43 LINK O LEU A 184 CA CA A 903 1555 1555 2.23 LINK NE2 HIS A 187 ZN ZN A 902 1555 1555 1.96 LINK O ASN A 194 CA CA A 904 1555 1555 2.79 LINK O GLY A 196 CA CA A 904 1555 1555 2.94 LINK OD1 ASP A 198 CA CA A 904 1555 1555 2.59 LINK ND1 HIS A 200 ZN ZN A 902 1555 1555 2.01 LINK OD2 ASP A 202 CA CA A 903 1555 1555 2.30 LINK O ASP A 203 CA CA A 905 1555 1555 2.82 LINK OD2 ASP A 203 CA CA A 905 1555 1555 3.13 LINK OE2 GLU A 205 CA CA A 903 1555 1555 2.23 LINK O GLU A 205 CA CA A 905 1555 1555 2.91 LINK NE2 HIS A 222 ZN ZN A 901 1555 1555 2.08 LINK NE2 HIS A 226 ZN ZN A 901 1555 1555 2.18 LINK NE2 HIS A 232 ZN ZN A 901 1555 1555 2.15 LINK ZN ZN A 901 O HOH A2159 1555 1555 1.98 LINK CA CA A 904 O HOH A2007 1555 1555 2.85 LINK CA CA A 904 O HOH A2266 1555 1555 2.45 LINK CA CA A 905 O HOH A2002 1555 1555 3.18 LINK O ASP B 162 CA CA B 904 1555 1555 2.95 LINK NE2 HIS B 172 ZN ZN B 902 1555 1555 2.07 LINK OD2 ASP B 174 ZN ZN B 902 1555 1555 1.90 LINK OD1 ASP B 179 CA CA B 903 1555 1555 2.44 LINK O GLY B 180 CA CA B 903 1555 1555 2.22 LINK O SER B 182 CA CA B 903 1555 1555 2.41 LINK O LEU B 184 CA CA B 903 1555 1555 2.16 LINK NE2 HIS B 187 ZN ZN B 902 1555 1555 2.06 LINK O ASN B 194 CA CA B 904 1555 1555 2.67 LINK O GLY B 196 CA CA B 904 1555 1555 3.08 LINK OD1 ASP B 198 CA CA B 904 1555 1555 2.64 LINK ND1 HIS B 200 ZN ZN B 902 1555 1555 2.12 LINK OD2 ASP B 202 CA CA B 903 1555 1555 2.52 LINK OE2 GLU B 205 CA CA B 903 1555 1555 2.38 LINK NE2 HIS B 222 ZN ZN B 901 1555 1555 2.08 LINK NE2 HIS B 226 ZN ZN B 901 1555 1555 2.08 LINK NE2 HIS B 232 ZN ZN B 901 1555 1555 2.02 LINK ZN ZN B 901 O HOH B2130 1555 1555 1.96 LINK CA CA B 904 O HOH B2026 1555 1555 3.15 LINK CA CA B 905 O HOH B2254 1555 1555 2.54 SITE 1 AC1 5 HIS A 222 HIS A 226 HIS A 232 HOH A2040 SITE 2 AC1 5 HOH A2159 SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC3 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC3 6 ASP A 202 GLU A 205 SITE 1 AC4 7 ALA A 161 ASP A 162 ASN A 194 GLY A 196 SITE 2 AC4 7 ASP A 198 HOH A2007 HOH A2266 SITE 1 AC5 3 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC6 23 LYS A 140 ASN A 215 PHE A 217 LEU A 218 SITE 2 AC6 23 VAL A 219 HIS A 222 ALA A 238 LEU A 239 SITE 3 AC6 23 PHE A 241 ILE A 243 TYR A 244 THR A 245 SITE 4 AC6 23 TYR A 246 THR A 247 LYS A 249 SER A 250 SITE 5 AC6 23 PRO A 255 HOH A2039 HOH A2062 HOH A2065 SITE 6 AC6 23 HOH A2094 HOH A2146 HOH A2208 SITE 1 AC7 5 HIS B 222 HIS B 226 HIS B 232 HOH B2079 SITE 2 AC7 5 HOH B2130 SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC9 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AC9 6 ASP B 202 GLU B 205 SITE 1 BC1 5 ALA B 161 ASP B 162 ASN B 194 GLY B 196 SITE 2 BC1 5 ASP B 198 SITE 1 BC2 4 ASP B 128 GLU B 205 THR B 206 HOH B2254 SITE 1 BC3 23 LYS B 140 ASN B 215 PHE B 217 LEU B 218 SITE 2 BC3 23 VAL B 219 HIS B 222 ALA B 238 LEU B 239 SITE 3 BC3 23 PHE B 241 PRO B 242 ILE B 243 TYR B 244 SITE 4 BC3 23 THR B 245 TYR B 246 THR B 247 LYS B 249 SITE 5 BC3 23 SER B 250 PRO B 255 HOH B2008 HOH B2101 SITE 6 BC3 23 HOH B2149 HOH B2166 HOH B2244 CRYST1 120.846 95.740 36.443 90.00 90.00 90.00 P 21 21 2 8 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 0.008275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027440 0.00000