HEADER HYDROLASE 24-AUG-23 8W4R TITLE CRYSTAL STRUCTURE OF PDE4D COMPLEXED WITH CVT-313 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PDE4D, DPDE3, PDE43; COMPND 5 EC: 3.1.4.53; 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: PDE4D, DPDE3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PDE4D, COMPLEX, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LIU,M.J.LI,Y.C.XU REVDAT 1 22-NOV-23 8W4R 0 JRNL AUTH J.LIU,X.ZHANG,G.CHEN,Q.SHAO,Y.ZOU,Z.LI,H.SU,M.LI,Y.XU JRNL TITL DRUG REPURPOSING AND STRUCTURE-BASED DISCOVERY OF NEW PDE4 JRNL TITL 2 AND PDE5 INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 262 15893 2023 JRNL REFN ISSN 0223-5234 JRNL PMID 37918035 JRNL DOI 10.1016/J.EJMECH.2023.115893 REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 162927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 15757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.3340 - 4.2531 0.98 9830 497 0.1840 0.1840 REMARK 3 2 4.2531 - 3.3773 0.99 9899 488 0.1880 0.1915 REMARK 3 3 3.3773 - 2.9508 1.00 9953 507 0.2036 0.2077 REMARK 3 4 2.9508 - 2.6812 1.00 9934 524 0.2084 0.2142 REMARK 3 5 2.6812 - 2.4891 1.00 10012 518 0.2070 0.2165 REMARK 3 6 2.4891 - 2.3424 1.00 10013 478 0.2066 0.2092 REMARK 3 7 2.3424 - 2.2251 1.00 9994 533 0.2036 0.2386 REMARK 3 8 2.2251 - 2.1283 0.99 9873 542 0.1955 0.1995 REMARK 3 9 2.1283 - 2.0464 1.00 9981 549 0.2092 0.2128 REMARK 3 10 2.0464 - 1.9758 1.00 9919 588 0.2178 0.2414 REMARK 3 11 1.9758 - 1.9140 1.00 10015 504 0.2189 0.2455 REMARK 3 12 1.9140 - 1.8593 1.00 9986 518 0.2100 0.2100 REMARK 3 13 1.8593 - 1.8104 1.00 9864 544 0.2154 0.2476 REMARK 3 14 1.8104 - 1.7662 1.00 10019 505 0.2122 0.2182 REMARK 3 15 1.7662 - 1.7260 1.00 9965 502 0.2151 0.2298 REMARK 3 16 1.7260 - 1.6893 1.00 9915 565 0.2191 0.2435 REMARK 3 17 1.6893 - 1.6555 1.00 9986 469 0.2260 0.2642 REMARK 3 18 1.6555 - 1.6243 1.00 9940 530 0.2148 0.2298 REMARK 3 19 1.6243 - 1.5953 1.00 10012 521 0.2100 0.2100 REMARK 3 20 1.5953 - 1.5682 0.99 9952 524 0.2323 0.2470 REMARK 3 21 1.5682 - 1.5429 1.00 9924 508 0.2300 0.2300 REMARK 3 22 1.5429 - 1.5192 1.00 9932 558 0.2433 0.2599 REMARK 3 23 1.5192 - 1.4969 1.00 9929 555 0.2549 0.2629 REMARK 3 24 1.4969 - 1.4758 1.00 9962 550 0.2548 0.2570 REMARK 3 25 1.4758 - 1.4558 1.00 10007 483 0.2673 0.2989 REMARK 3 26 1.4558 - 1.4369 1.00 9903 530 0.2782 0.2897 REMARK 3 27 1.4369 - 1.4190 1.00 9935 533 0.2828 0.3132 REMARK 3 28 1.4190 - 1.4019 1.00 9967 530 0.3055 0.3240 REMARK 3 29 1.4019 - 1.3856 0.99 9844 535 0.3186 0.3267 REMARK 3 30 1.3856 - 1.3700 1.00 9936 569 0.3317 0.3536 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 5304 REMARK 3 ANGLE : 0.708 7210 REMARK 3 CHIRALITY : 0.063 839 REMARK 3 PLANARITY : 0.004 921 REMARK 3 DIHEDRAL : 5.253 1924 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.1886 83.6686 46.7141 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1364 REMARK 3 T33: 0.1951 T12: 0.0013 REMARK 3 T13: 0.0368 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.3438 L22: 0.6281 REMARK 3 L33: 2.5291 L12: -0.1832 REMARK 3 L13: 0.1467 L23: 0.2512 REMARK 3 S TENSOR REMARK 3 S11: -0.0580 S12: -0.0506 S13: -0.0188 REMARK 3 S21: 0.1071 S22: 0.0706 S23: 0.0040 REMARK 3 S31: 0.1801 S32: 0.1023 S33: -0.0179 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8W4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300040097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 162983 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 REMARK 200 RESOLUTION RANGE LOW (A) : 30.334 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.2 M MGCL2, 10 % (V/V) REMARK 280 ISOPROPANOL, 30 % (V/V) ETHYLENE GLYCOL, 18 % (W/V) PEG 3350, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.31500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.83500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.35500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.83500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.31500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.35500 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 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 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 65 REMARK 465 GLY A 66 REMARK 465 SER A 67 REMARK 465 SER A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 GLY A 77 REMARK 465 LEU A 78 REMARK 465 VAL A 79 REMARK 465 PRO A 80 REMARK 465 ARG A 81 REMARK 465 GLY A 82 REMARK 465 SER A 83 REMARK 465 HIS A 84 REMARK 465 MET A 85 REMARK 465 THR A 86 REMARK 465 GLU A 87 REMARK 465 PRO A 411 REMARK 465 GLN A 412 REMARK 465 SER A 413 REMARK 465 MET B 65 REMARK 465 GLY B 66 REMARK 465 SER B 67 REMARK 465 SER B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 HIS B 71 REMARK 465 HIS B 72 REMARK 465 HIS B 73 REMARK 465 HIS B 74 REMARK 465 SER B 75 REMARK 465 SER B 76 REMARK 465 GLY B 77 REMARK 465 LEU B 78 REMARK 465 VAL B 79 REMARK 465 PRO B 80 REMARK 465 ARG B 81 REMARK 465 GLY B 82 REMARK 465 SER B 83 REMARK 465 HIS B 84 REMARK 465 MET B 85 REMARK 465 THR B 86 REMARK 465 GLU B 87 REMARK 465 PRO B 411 REMARK 465 GLN B 412 REMARK 465 SER B 413 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 GLU A 89 CG CD OE1 OE2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 SER A 295 OG REMARK 470 ARG A 342 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 GLN B 88 CG CD OE1 NE2 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 GLU B 97 CG CD OE1 OE2 REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 LYS B 133 CG CD CE NZ REMARK 470 GLU B 182 CG CD OE1 OE2 REMARK 470 LYS B 239 CG CD CE NZ REMARK 470 GLU B 244 CG CD OE1 OE2 REMARK 470 THR B 253 OG1 CG2 REMARK 470 LYS B 254 CG CD CE NZ REMARK 470 LYS B 255 CG CD CE NZ REMARK 470 GLN B 256 CG CD OE1 NE2 REMARK 470 GLN B 258 CG CD OE1 NE2 REMARK 470 GLU B 288 CG CD OE1 OE2 REMARK 470 GLU B 338 CG CD OE1 OE2 REMARK 470 ARG B 342 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 349 CG CD OE1 OE2 REMARK 470 GLU B 353 CG CD OE1 OE2 REMARK 470 ASP B 391 CG OD1 OD2 REMARK 470 GLU B 400 CG CD OE1 OE2 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 ASN A 362 -3.95 -141.50 REMARK 500 ILE A 376 -60.17 -125.61 REMARK 500 ASN B 161 -168.51 -127.18 REMARK 500 ILE B 376 -58.42 -123.65 REMARK 500 HIS B 389 122.14 -39.91 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 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 164 NE2 REMARK 620 2 HIS A 200 NE2 95.4 REMARK 620 3 ASP A 201 OD2 89.4 85.4 REMARK 620 4 ASP A 318 OD2 91.1 89.1 174.5 REMARK 620 5 HOH A 602 O 168.3 96.2 89.6 91.0 REMARK 620 6 HOH A 669 O 89.1 174.6 97.5 87.9 79.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 201 OD1 REMARK 620 2 HOH A 602 O 93.0 REMARK 620 3 HOH A 619 O 84.3 96.7 REMARK 620 4 HOH A 629 O 169.2 94.4 86.9 REMARK 620 5 HOH A 662 O 88.7 169.6 93.7 85.5 REMARK 620 6 HOH A 694 O 99.3 81.3 175.9 89.7 88.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 97.1 REMARK 620 3 ASP B 201 OD2 88.2 85.3 REMARK 620 4 ASP B 318 OD1 91.9 88.3 173.6 REMARK 620 5 HOH B 601 O 167.4 95.3 91.0 90.3 REMARK 620 6 HOH B 648 O 89.0 172.9 98.5 87.9 78.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 601 O 92.2 REMARK 620 3 HOH B 613 O 84.6 95.1 REMARK 620 4 HOH B 621 O 169.2 93.8 85.9 REMARK 620 5 HOH B 642 O 88.9 171.2 93.8 86.6 REMARK 620 6 HOH B 661 O 99.8 81.5 174.5 90.0 89.7 REMARK 620 N 1 2 3 4 5 DBREF 8W4R A 86 413 UNP Q08499 PDE4D_HUMAN 388 715 DBREF 8W4R B 86 413 UNP Q08499 PDE4D_HUMAN 388 715 SEQADV 8W4R MET A 65 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY A 66 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER A 67 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER A 68 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 69 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 70 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 71 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 72 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 73 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 74 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER A 75 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER A 76 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY A 77 UNP Q08499 EXPRESSION TAG SEQADV 8W4R LEU A 78 UNP Q08499 EXPRESSION TAG SEQADV 8W4R VAL A 79 UNP Q08499 EXPRESSION TAG SEQADV 8W4R PRO A 80 UNP Q08499 EXPRESSION TAG SEQADV 8W4R ARG A 81 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY A 82 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER A 83 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS A 84 UNP Q08499 EXPRESSION TAG SEQADV 8W4R MET A 85 UNP Q08499 EXPRESSION TAG SEQADV 8W4R MET B 65 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY B 66 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER B 67 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER B 68 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 69 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 70 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 71 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 72 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 73 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 74 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER B 75 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER B 76 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY B 77 UNP Q08499 EXPRESSION TAG SEQADV 8W4R LEU B 78 UNP Q08499 EXPRESSION TAG SEQADV 8W4R VAL B 79 UNP Q08499 EXPRESSION TAG SEQADV 8W4R PRO B 80 UNP Q08499 EXPRESSION TAG SEQADV 8W4R ARG B 81 UNP Q08499 EXPRESSION TAG SEQADV 8W4R GLY B 82 UNP Q08499 EXPRESSION TAG SEQADV 8W4R SER B 83 UNP Q08499 EXPRESSION TAG SEQADV 8W4R HIS B 84 UNP Q08499 EXPRESSION TAG SEQADV 8W4R MET B 85 UNP Q08499 EXPRESSION TAG SEQRES 1 A 349 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 349 LEU VAL PRO ARG GLY SER HIS MET THR GLU GLN GLU ASP SEQRES 3 A 349 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 4 A 349 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 5 A 349 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 6 A 349 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 7 A 349 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 8 A 349 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 9 A 349 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 10 A 349 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 11 A 349 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 12 A 349 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 13 A 349 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 14 A 349 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 15 A 349 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 16 A 349 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 17 A 349 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 18 A 349 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 19 A 349 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 20 A 349 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 21 A 349 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 22 A 349 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 23 A 349 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 24 A 349 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 25 A 349 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 26 A 349 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 27 A 349 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER SEQRES 1 B 349 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 349 LEU VAL PRO ARG GLY SER HIS MET THR GLU GLN GLU ASP SEQRES 3 B 349 VAL LEU ALA LYS GLU LEU GLU ASP VAL ASN LYS TRP GLY SEQRES 4 B 349 LEU HIS VAL PHE ARG ILE ALA GLU LEU SER GLY ASN ARG SEQRES 5 B 349 PRO LEU THR VAL ILE MET HIS THR ILE PHE GLN GLU ARG SEQRES 6 B 349 ASP LEU LEU LYS THR PHE LYS ILE PRO VAL ASP THR LEU SEQRES 7 B 349 ILE THR TYR LEU MET THR LEU GLU ASP HIS TYR HIS ALA SEQRES 8 B 349 ASP VAL ALA TYR HIS ASN ASN ILE HIS ALA ALA ASP VAL SEQRES 9 B 349 VAL GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 10 B 349 GLU ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 11 B 349 PHE ALA SER ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 12 B 349 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 13 B 349 LEU MET TYR ASN ASP SER SER VAL LEU GLU ASN HIS HIS SEQRES 14 B 349 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU ASN CYS SEQRES 15 B 349 ASP ILE PHE GLN ASN LEU THR LYS LYS GLN ARG GLN SER SEQRES 16 B 349 LEU ARG LYS MET VAL ILE ASP ILE VAL LEU ALA THR ASP SEQRES 17 B 349 MET SER LYS HIS MET ASN LEU LEU ALA ASP LEU LYS THR SEQRES 18 B 349 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 19 B 349 LEU LEU ASP ASN TYR SER ASP ARG ILE GLN VAL LEU GLN SEQRES 20 B 349 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 21 B 349 PRO LEU GLN LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 22 B 349 GLU GLU PHE PHE ARG GLN GLY ASP ARG GLU ARG GLU ARG SEQRES 23 B 349 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS ASN ALA SEQRES 24 B 349 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 25 B 349 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL HIS SEQRES 26 B 349 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 27 B 349 ARG GLU TRP TYR GLN SER THR ILE PRO GLN SER HET AJR A 501 29 HET MG A 502 1 HET ZN A 503 1 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HET AJR B 501 29 HET MG B 502 1 HET ZN B 503 1 HET EDO B 504 4 HET EDO B 505 4 HET EDO B 506 4 HETNAM AJR 2,2'-{[6-{[(4-METHOXYPHENYL)METHYL]AMINO}-9-(PROPAN-2- HETNAM 2 AJR YL)-9H-PURIN-2-YL]AZANEDIYL}DI(ETHAN-1-OL) HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 AJR 2(C20 H28 N6 O3) FORMUL 4 MG 2(MG 2+) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 EDO 8(C2 H6 O2) FORMUL 17 HOH *206(H2 O) HELIX 1 AA1 GLN A 88 GLU A 97 1 10 HELIX 2 AA2 HIS A 105 SER A 113 1 9 HELIX 3 AA3 ARG A 116 ARG A 129 1 14 HELIX 4 AA4 ASP A 130 LYS A 136 1 7 HELIX 5 AA5 PRO A 138 HIS A 152 1 15 HELIX 6 AA6 ASN A 161 SER A 177 1 17 HELIX 7 AA7 THR A 178 GLU A 182 5 5 HELIX 8 AA8 THR A 186 HIS A 200 1 15 HELIX 9 AA9 SER A 208 THR A 215 1 8 HELIX 10 AB1 SER A 217 ASN A 224 1 8 HELIX 11 AB2 SER A 227 LEU A 240 1 14 HELIX 12 AB3 LEU A 241 GLU A 243 5 3 HELIX 13 AB4 THR A 253 ALA A 270 1 18 HELIX 14 AB5 THR A 271 SER A 274 5 4 HELIX 15 AB6 LYS A 275 THR A 289 1 15 HELIX 16 AB7 ASN A 302 LEU A 319 1 18 HELIX 17 AB8 SER A 320 LYS A 324 5 5 HELIX 18 AB9 PRO A 325 ARG A 350 1 26 HELIX 19 AC1 SER A 364 ILE A 376 1 13 HELIX 20 AC2 ILE A 376 VAL A 388 1 13 HELIX 21 AC3 ALA A 392 ILE A 410 1 19 HELIX 22 AC4 GLU B 89 LEU B 96 1 8 HELIX 23 AC5 GLU B 97 VAL B 99 5 3 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ARG B 129 1 14 HELIX 26 AC8 ASP B 130 PHE B 135 1 6 HELIX 27 AC9 PRO B 138 HIS B 152 1 15 HELIX 28 AD1 ASN B 161 SER B 177 1 17 HELIX 29 AD2 THR B 178 GLU B 182 5 5 HELIX 30 AD3 THR B 186 HIS B 200 1 15 HELIX 31 AD4 SER B 208 THR B 215 1 8 HELIX 32 AD5 SER B 217 ASN B 224 1 8 HELIX 33 AD6 SER B 227 LEU B 240 1 14 HELIX 34 AD7 LEU B 241 GLU B 243 5 3 HELIX 35 AD8 THR B 253 ALA B 270 1 18 HELIX 36 AD9 THR B 271 SER B 274 5 4 HELIX 37 AE1 LYS B 275 THR B 289 1 15 HELIX 38 AE2 ASN B 302 LEU B 319 1 18 HELIX 39 AE3 SER B 320 LYS B 324 5 5 HELIX 40 AE4 PRO B 325 ARG B 350 1 26 HELIX 41 AE5 SER B 364 ILE B 376 1 13 HELIX 42 AE6 ILE B 376 VAL B 388 1 13 HELIX 43 AE7 ALA B 392 THR B 409 1 18 LINK NE2 HIS A 164 ZN ZN A 503 1555 1555 2.18 LINK NE2 HIS A 200 ZN ZN A 503 1555 1555 2.21 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.03 LINK OD2 ASP A 201 ZN ZN A 503 1555 1555 2.05 LINK OD2 ASP A 318 ZN ZN A 503 1555 1555 2.12 LINK MG MG A 502 O HOH A 602 1555 1555 2.14 LINK MG MG A 502 O HOH A 619 1555 1555 2.12 LINK MG MG A 502 O HOH A 629 1555 1555 2.11 LINK MG MG A 502 O HOH A 662 1555 1555 2.10 LINK MG MG A 502 O HOH A 694 1555 1555 2.13 LINK ZN ZN A 503 O HOH A 602 1555 1555 2.09 LINK ZN ZN A 503 O HOH A 669 1555 1555 2.18 LINK NE2 HIS B 164 ZN ZN B 503 1555 1555 2.18 LINK NE2 HIS B 200 ZN ZN B 503 1555 1555 2.20 LINK OD1 ASP B 201 MG MG B 502 1555 1555 2.07 LINK OD2 ASP B 201 ZN ZN B 503 1555 1555 2.07 LINK OD1 ASP B 318 ZN ZN B 503 1555 1555 2.12 LINK MG MG B 502 O HOH B 601 1555 1555 2.17 LINK MG MG B 502 O HOH B 613 1555 1555 2.17 LINK MG MG B 502 O HOH B 621 1555 1555 2.13 LINK MG MG B 502 O HOH B 642 1555 1555 2.09 LINK MG MG B 502 O HOH B 661 1555 1555 2.14 LINK ZN ZN B 503 O HOH B 601 1555 1555 2.11 LINK ZN ZN B 503 O HOH B 648 1555 1555 2.18 CISPEP 1 HIS A 389 PRO A 390 0 0.33 CISPEP 2 HIS B 389 PRO B 390 0 2.10 CRYST1 58.630 80.710 163.670 90.00 90.00 90.00 P 21 21 21 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 0.017056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006110 0.00000