HEADER HYDROLASE 19-MAR-13 4JPA TITLE MMP13 IN COMPLEX WITH A PIPERAZINE HYDANTOIN LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 103-274; 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_TAXID: 9606; SOURCE 4 GENE: MMP13; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MATRIX METALLOPROTEASE, CALCIUM BINDING, ZINC BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GERHARDT,D.HARGREAVES REVDAT 3 20-MAR-24 4JPA 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4JPA 1 REMARK REVDAT 1 05-MAR-14 4JPA 0 JRNL AUTH C.DE SAVI,D.WATERSON,A.PAPE,S.LAMONT,E.HADLEY,M.MILLS, JRNL AUTH 2 K.M.PAGE,J.BOWYER,R.A.MACIEWICZ JRNL TITL HYDANTOIN BASED INHIBITORS OF MMP13--DISCOVERY OF AZD6605. JRNL REF BIOORG.MED.CHEM.LETT. V. 23 4705 2013 JRNL REFN ISSN 0960-894X JRNL PMID 23810497 JRNL DOI 10.1016/J.BMCL.2013.05.089 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 21114 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1140 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1475 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2641 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 373 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -1.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.77000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.549 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2810 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2297 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3827 ; 1.207 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5376 ; 0.717 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 5.920 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;36.383 ;23.985 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;13.500 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.685 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 375 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3184 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 596 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 601 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2243 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1367 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1388 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.123 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 29 ; 0.119 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 17 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 86 ; 0.195 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.120 ; 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): 1645 ; 0.381 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 673 ; 0.062 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2647 ; 0.713 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1217 ; 0.952 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 1.427 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 8 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 104 A 272 REMARK 3 RESIDUE RANGE : B 104 B 269 REMARK 3 RESIDUE RANGE : A 301 A 305 REMARK 3 RESIDUE RANGE : B 301 B 305 REMARK 3 RESIDUE RANGE : A 306 A 306 REMARK 3 RESIDUE RANGE : B 306 B 306 REMARK 3 RESIDUE RANGE : A 401 A 589 REMARK 3 RESIDUE RANGE : B 401 B 584 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0860 0.1641 20.7925 REMARK 3 T TENSOR REMARK 3 T11: -0.0180 T22: -0.0333 REMARK 3 T33: -0.0018 T12: -0.0036 REMARK 3 T13: -0.0018 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.2552 L22: 0.0910 REMARK 3 L33: 0.2516 L12: -0.0489 REMARK 3 L13: -0.0101 L23: 0.0154 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: 0.0088 S13: -0.0003 REMARK 3 S21: -0.0157 S22: -0.0082 S23: 0.0140 REMARK 3 S31: -0.0116 S32: 0.0103 S33: -0.0058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 4JPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000078332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA, SCALEPACK, D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23627 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27.5% PEG 4000 1.25M AMFORMATE, 100MM REMARK 280 TRISHCL PH 8.5 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 67.38550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.99300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.38550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.99300 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 436 LIES ON A SPECIAL POSITION. 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 102 REMARK 465 GLU A 103 REMARK 465 THR A 247 REMARK 465 GLY A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 PRO A 273 REMARK 465 ASN A 274 REMARK 465 MET B 102 REMARK 465 GLU B 103 REMARK 465 ASP B 270 REMARK 465 GLU B 271 REMARK 465 ASP B 272 REMARK 465 PRO B 273 REMARK 465 ASN B 274 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 -129.88 44.34 REMARK 500 SER A 182 -166.03 58.02 REMARK 500 ASN A 194 -114.00 57.81 REMARK 500 SER A 210 -160.36 -123.84 REMARK 500 ASP A 231 -156.02 -96.03 REMARK 500 PRO A 242 49.15 -78.62 REMARK 500 LYS B 170 -131.88 47.39 REMARK 500 TYR B 176 70.40 -111.24 REMARK 500 SER B 182 -172.34 68.61 REMARK 500 ASN B 194 -119.57 59.14 REMARK 500 SER B 210 -117.19 -119.10 REMARK 500 PRO B 242 47.74 -78.33 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 A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 203 O 162.4 REMARK 620 3 ASP A 203 OD2 94.1 70.9 REMARK 620 4 GLU A 205 O 81.7 94.2 108.7 REMARK 620 5 HOH A 526 O 115.5 78.5 106.4 139.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 174.5 REMARK 620 3 GLY A 196 O 90.9 94.6 REMARK 620 4 ASP A 198 OD1 83.8 97.0 91.6 REMARK 620 5 HOH A 402 O 91.8 88.1 81.1 171.4 REMARK 620 6 HOH A 584 O 93.1 81.4 171.1 96.7 90.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 114.2 REMARK 620 3 HIS A 187 NE2 116.7 113.3 REMARK 620 4 HIS A 200 ND1 110.6 91.5 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 92.0 REMARK 620 3 SER A 182 O 86.9 90.0 REMARK 620 4 LEU A 184 O 85.0 172.6 96.5 REMARK 620 5 ASP A 202 OD2 91.6 86.2 175.9 87.1 REMARK 620 6 GLU A 205 OE2 169.5 97.3 88.3 86.3 93.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 100.4 REMARK 620 3 HIS A 232 NE2 112.7 101.5 REMARK 620 4 AZ6 A 306 N7 113.6 124.3 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 128 OD2 REMARK 620 2 ASP B 203 OD2 99.8 REMARK 620 3 ASP B 203 O 166.3 71.4 REMARK 620 4 GLU B 205 O 83.2 110.1 90.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 173.5 REMARK 620 3 GLY B 196 O 91.4 94.6 REMARK 620 4 ASP B 198 OD1 85.5 96.5 92.0 REMARK 620 5 HOH B 427 O 87.7 91.7 75.1 165.3 REMARK 620 6 HOH B 428 O 89.4 84.2 166.6 101.4 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 112.6 REMARK 620 3 HIS B 187 NE2 113.5 116.9 REMARK 620 4 HIS B 200 ND1 104.7 90.0 116.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 85.8 REMARK 620 3 SER B 182 O 86.3 85.5 REMARK 620 4 LEU B 184 O 90.3 175.6 96.4 REMARK 620 5 ASP B 202 OD2 93.4 86.9 172.4 91.2 REMARK 620 6 GLU B 205 OE2 173.9 92.8 87.6 91.2 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 97.4 REMARK 620 3 HIS B 232 NE2 107.5 105.1 REMARK 620 4 AZ6 B 306 N7 116.5 121.2 108.0 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZ6 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZ6 B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JP4 RELATED DB: PDB REMARK 900 MMP13 IN COMPLEX WITH AZD6605 DBREF 4JPA A 103 274 UNP P45452 MMP13_HUMAN 103 274 DBREF 4JPA B 103 274 UNP P45452 MMP13_HUMAN 103 274 SEQADV 4JPA MET A 102 UNP P45452 EXPRESSION TAG SEQADV 4JPA MET B 102 UNP P45452 EXPRESSION TAG SEQRES 1 A 173 MET GLU TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER SEQRES 2 A 173 LYS MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO SEQRES 3 A 173 ASP MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS SEQRES 4 A 173 ALA PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE SEQRES 5 A 173 THR ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER SEQRES 6 A 173 PHE GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP SEQRES 7 A 173 GLY PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY SEQRES 8 A 173 PRO ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU SEQRES 9 A 173 THR TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU SEQRES 10 A 173 VAL ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP SEQRES 11 A 173 HIS SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR SEQRES 12 A 173 THR TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP SEQRES 13 A 173 ASP VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP SEQRES 14 A 173 GLU ASP PRO ASN SEQRES 1 B 173 MET GLU TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER SEQRES 2 B 173 LYS MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO SEQRES 3 B 173 ASP MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS SEQRES 4 B 173 ALA PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE SEQRES 5 B 173 THR ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER SEQRES 6 B 173 PHE GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP SEQRES 7 B 173 GLY PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY SEQRES 8 B 173 PRO ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU SEQRES 9 B 173 THR TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU SEQRES 10 B 173 VAL ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP SEQRES 11 B 173 HIS SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR SEQRES 12 B 173 THR TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP SEQRES 13 B 173 ASP VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP SEQRES 14 B 173 GLU ASP PRO ASN HET ZN A 301 1 HET CA A 302 1 HET ZN A 303 1 HET CA A 304 1 HET NA A 305 1 HET AZ6 A 306 34 HET ZN B 301 1 HET ZN B 302 1 HET CA B 303 1 HET CA B 304 1 HET NA B 305 1 HET AZ6 B 306 34 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM AZ6 3-[({2-[4-({[(4S)-4-METHYL-2,5-DIOXOIMIDAZOLIDIN-4- HETNAM 2 AZ6 YL]METHYL}SULFONYL)PIPERAZIN-1-YL]PYRIMIDIN-5-YL}OXY) HETNAM 3 AZ6 METHYL]BENZONITRILE FORMUL 3 ZN 4(ZN 2+) FORMUL 4 CA 4(CA 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 AZ6 2(C21 H23 N7 O5 S) FORMUL 15 HOH *373(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 ARG A 155 0 SHEET 2 A 5 ASN A 117 ILE A 122 1 N LEU A 118 O ASN A 152 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 GLY A 168 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 LEU B 156 0 SHEET 2 C 5 ASN B 117 ILE B 122 1 N TYR B 120 O LEU B 156 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 PHE B 201 N SER B 166 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 NA NA A 305 1555 1555 2.53 LINK O ASP A 162 CA CA A 302 1555 1555 2.42 LINK NE2 HIS A 172 ZN ZN A 303 1555 1555 2.06 LINK OD2 ASP A 174 ZN ZN A 303 1555 1555 1.96 LINK OD1 ASP A 179 CA CA A 304 1555 1555 2.46 LINK O GLY A 180 CA CA A 304 1555 1555 2.22 LINK O SER A 182 CA CA A 304 1555 1555 2.37 LINK O LEU A 184 CA CA A 304 1555 1555 2.34 LINK NE2 HIS A 187 ZN ZN A 303 1555 1555 2.04 LINK O ASN A 194 CA CA A 302 1555 1555 2.29 LINK O GLY A 196 CA CA A 302 1555 1555 2.31 LINK OD1 ASP A 198 CA CA A 302 1555 1555 2.47 LINK ND1 HIS A 200 ZN ZN A 303 1555 1555 2.08 LINK OD2 ASP A 202 CA CA A 304 1555 1555 2.22 LINK O ASP A 203 NA NA A 305 1555 1555 2.61 LINK OD2 ASP A 203 NA NA A 305 1555 1555 2.64 LINK OE2 GLU A 205 CA CA A 304 1555 1555 2.16 LINK O GLU A 205 NA NA A 305 1555 1555 2.44 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.10 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.08 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.07 LINK ZN ZN A 301 N7 AZ6 A 306 1555 1555 2.04 LINK CA CA A 302 O HOH A 402 1555 1555 2.32 LINK CA CA A 302 O HOH A 584 1555 1555 2.37 LINK NA NA A 305 O HOH A 526 1555 1555 2.65 LINK OD2 ASP B 128 NA NA B 305 1555 1555 2.34 LINK O ASP B 162 CA CA B 303 1555 1555 2.27 LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 2.05 LINK OD2 ASP B 174 ZN ZN B 302 1555 1555 1.94 LINK OD1 ASP B 179 CA CA B 304 1555 1555 2.34 LINK O GLY B 180 CA CA B 304 1555 1555 2.35 LINK O SER B 182 CA CA B 304 1555 1555 2.36 LINK O LEU B 184 CA CA B 304 1555 1555 2.29 LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 2.20 LINK O ASN B 194 CA CA B 303 1555 1555 2.28 LINK O GLY B 196 CA CA B 303 1555 1555 2.40 LINK OD1 ASP B 198 CA CA B 303 1555 1555 2.49 LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.09 LINK OD2 ASP B 202 CA CA B 304 1555 1555 2.32 LINK OD2 ASP B 203 NA NA B 305 1555 1555 2.61 LINK O ASP B 203 NA NA B 305 1555 1555 2.68 LINK OE2 GLU B 205 CA CA B 304 1555 1555 2.19 LINK O GLU B 205 NA NA B 305 1555 1555 2.41 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.12 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.08 LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.04 LINK ZN ZN B 301 N7 AZ6 B 306 1555 1555 2.05 LINK CA CA B 303 O HOH B 427 1555 1555 2.39 LINK CA CA B 303 O HOH B 428 1555 1555 2.18 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 AZ6 A 306 SITE 1 AC2 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC2 6 HOH A 402 HOH A 584 SITE 1 AC3 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC4 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC4 6 ASP A 202 GLU A 205 SITE 1 AC5 4 ASP A 128 ASP A 203 GLU A 205 HOH A 526 SITE 1 AC6 20 LEU A 184 LEU A 185 ALA A 186 HIS A 187 SITE 2 AC6 20 LEU A 218 HIS A 222 GLU A 223 HIS A 226 SITE 3 AC6 20 HIS A 232 GLY A 237 ALA A 238 LEU A 239 SITE 4 AC6 20 PHE A 241 PRO A 242 ILE A 243 TYR A 244 SITE 5 AC6 20 THR A 245 TYR A 246 ZN A 301 HOH A 445 SITE 1 AC7 4 HIS B 222 HIS B 226 HIS B 232 AZ6 B 306 SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC9 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 AC9 6 HOH B 427 HOH B 428 SITE 1 BC1 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 BC1 6 ASP B 202 GLU B 205 SITE 1 BC2 4 HOH A 529 ASP B 128 ASP B 203 GLU B 205 SITE 1 BC3 20 GLY B 183 LEU B 185 ALA B 186 LEU B 218 SITE 2 BC3 20 HIS B 222 GLU B 223 HIS B 226 HIS B 232 SITE 3 BC3 20 ALA B 238 LEU B 239 PHE B 241 ILE B 243 SITE 4 BC3 20 TYR B 244 THR B 245 TYR B 246 THR B 247 SITE 5 BC3 20 ZN B 301 HOH B 507 HOH B 513 HOH B 560 CRYST1 134.771 35.986 101.492 90.00 134.99 90.00 C 1 2 1 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 0.007420 0.000000 0.007417 0.00000 SCALE2 0.000000 0.027789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013932 0.00000