HEADER HYDROLASE/HYDROLASE INHIBITOR 24-OCT-18 6IND TITLE CRYSTAL STRUCTURE OF PDE4D COMPLEXED WITH A NOVEL INHIBITOR 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, INHIBITOR, COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHANG,H.X.SU,Y.C.XU REVDAT 2 27-MAR-24 6IND 1 LINK REVDAT 1 23-OCT-19 6IND 0 JRNL AUTH X.ZHANG,G.DONG,H.LI,W.CHEN,J.LI,C.FENG,Z.GU,F.ZHU,R.ZHANG, JRNL AUTH 2 M.LI,W.TANG,H.LIU,Y.XU JRNL TITL STRUCTURE-AIDED IDENTIFICATION AND OPTIMIZATION OF JRNL TITL 2 TETRAHYDRO-ISOQUINOLINES AS NOVEL PDE4 INHIBITORS LEADING TO JRNL TITL 3 DISCOVERY OF AN EFFECTIVE ANTIPSORIASIS AGENT. JRNL REF J.MED.CHEM. V. 62 5579 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31099559 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00518 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 62553 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) : 0.206 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3122 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 40.6845 - 5.2422 0.99 2918 167 0.1997 0.2166 REMARK 3 2 5.2422 - 4.1622 1.00 2806 143 0.1789 0.1984 REMARK 3 3 4.1622 - 3.6364 1.00 2771 150 0.1806 0.1891 REMARK 3 4 3.6364 - 3.3041 0.99 2794 132 0.1978 0.2320 REMARK 3 5 3.3041 - 3.0674 0.99 2714 152 0.1997 0.2749 REMARK 3 6 3.0674 - 2.8866 0.99 2733 130 0.2062 0.2308 REMARK 3 7 2.8866 - 2.7421 0.99 2729 141 0.2089 0.2452 REMARK 3 8 2.7421 - 2.6227 0.99 2695 156 0.2092 0.2482 REMARK 3 9 2.6227 - 2.5218 0.99 2696 139 0.2150 0.2960 REMARK 3 10 2.5218 - 2.4348 0.99 2699 141 0.2124 0.2376 REMARK 3 11 2.4348 - 2.3586 0.99 2691 129 0.2115 0.2480 REMARK 3 12 2.3586 - 2.2912 0.99 2671 145 0.2150 0.2706 REMARK 3 13 2.2912 - 2.2309 0.99 2680 134 0.2108 0.2264 REMARK 3 14 2.2309 - 2.1765 0.98 2719 129 0.2130 0.2522 REMARK 3 15 2.1765 - 2.1270 0.98 2635 157 0.2156 0.2630 REMARK 3 16 2.1270 - 2.0817 0.98 2648 151 0.2329 0.2551 REMARK 3 17 2.0817 - 2.0401 0.98 2656 146 0.2360 0.2950 REMARK 3 18 2.0401 - 2.0016 0.98 2638 132 0.2347 0.2844 REMARK 3 19 2.0016 - 1.9659 0.98 2664 148 0.2472 0.2920 REMARK 3 20 1.9659 - 1.9325 0.98 2625 129 0.2590 0.2843 REMARK 3 21 1.9325 - 1.9014 0.98 2642 123 0.2702 0.3445 REMARK 3 22 1.9014 - 1.8721 0.97 2607 148 0.2861 0.3161 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.190 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 : 0.007 5256 REMARK 3 ANGLE : 0.761 7157 REMARK 3 CHIRALITY : 0.046 832 REMARK 3 PLANARITY : 0.005 916 REMARK 3 DIHEDRAL : 5.561 3146 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6IND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-16 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.872 REMARK 200 RESOLUTION RANGE LOW (A) : 40.675 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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: NULL 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 (%): 47.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 0.2 M MGCL2, 10% REMARK 280 ISOPROPANOL, 30% EG, 18% PEG 3350, PH 7.0, VAPOR DIFFUSION, REMARK 280 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 28.91750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.66700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.09250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.66700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.91750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.09250 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 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 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 GLN B 88 REMARK 465 GLU B 89 REMARK 465 ASP B 90 REMARK 465 SER B 294 REMARK 465 SER B 295 REMARK 465 GLY B 296 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 87 CG CD OE1 OE2 REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 ASP A 90 CB CG OD1 OD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 LYS A 239 CE NZ REMARK 470 LYS A 254 CD CE NZ REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 ARG A 342 NE CZ NH1 NH2 REMARK 470 GLU A 349 CG CD OE1 OE2 REMARK 470 GLU A 353 CG CD OE1 OE2 REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 LYS B 94 CB CG CD CE NZ REMARK 470 ASP B 98 CG OD1 OD2 REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 ARG B 108 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 ILE B 121 CD1 REMARK 470 ASP B 130 CB CG OD1 OD2 REMARK 470 LYS B 133 CB CG CD CE NZ REMARK 470 LYS B 136 CB CG CD CE NZ REMARK 470 GLU B 182 CB CG CD OE1 OE2 REMARK 470 LYS B 239 CE NZ REMARK 470 GLU B 244 CG CD OE1 OE2 REMARK 470 LYS B 254 CD CE NZ REMARK 470 LYS B 255 CG CD CE NZ REMARK 470 GLU B 288 CG CD OE1 OE2 REMARK 470 LYS B 290 CG CD CE NZ REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 GLN B 327 CG CD OE1 NE2 REMARK 470 ARG B 342 NE CZ NH1 NH2 REMARK 470 GLU B 349 CG CD OE1 OE2 REMARK 470 GLU B 353 CG CD OE1 OE2 REMARK 470 ILE B 354 CD1 REMARK 470 ASP B 391 CG OD1 OD2 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 OE2 GLU A 382 C1 EDO A 505 1.37 REMARK 500 O HOH A 735 O HOH A 751 2.17 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 LEU A 104 138.91 -37.77 REMARK 500 ASN A 161 -168.97 -123.63 REMARK 500 SER A 227 54.65 38.58 REMARK 500 ASN A 362 48.96 -143.34 REMARK 500 ILE A 376 -58.61 -123.51 REMARK 500 ASN B 161 -168.46 -124.85 REMARK 500 ALA B 183 31.85 36.88 REMARK 500 ASN B 362 55.24 -163.38 REMARK 500 ILE B 376 -60.99 -120.71 REMARK 500 HIS B 389 119.29 -29.29 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 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 151 O REMARK 620 2 TYR A 153 O 97.0 REMARK 620 3 HOH A 707 O 95.8 52.4 REMARK 620 4 ASP B 301 OD1 94.1 49.4 3.6 REMARK 620 5 HOH B 602 O 95.2 51.6 1.1 2.6 REMARK 620 6 HOH B 627 O 96.9 48.0 4.4 3.0 3.8 REMARK 620 N 1 2 3 4 5 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 96.7 REMARK 620 3 ASP A 201 OD2 88.2 85.7 REMARK 620 4 ASP A 318 OD1 88.1 89.7 173.8 REMARK 620 5 HOH A 620 O 168.6 94.3 89.6 95.0 REMARK 620 6 HOH A 716 O 90.2 172.7 97.0 88.0 79.0 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 620 O 96.4 REMARK 620 3 HOH A 650 O 86.3 95.2 REMARK 620 4 HOH A 661 O 169.5 91.5 86.1 REMARK 620 5 HOH A 685 O 88.5 172.2 91.0 84.4 REMARK 620 6 HOH A 726 O 98.1 81.7 174.8 89.8 91.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 164 NE2 REMARK 620 2 HIS B 200 NE2 94.1 REMARK 620 3 ASP B 201 OD2 88.2 83.4 REMARK 620 4 ASP B 318 OD1 89.2 90.5 173.2 REMARK 620 5 HOH B 606 O 166.1 99.8 92.6 91.4 REMARK 620 6 HOH B 655 O 90.2 174.4 100.5 85.9 76.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 201 OD1 REMARK 620 2 HOH B 606 O 97.4 REMARK 620 3 HOH B 607 O 79.5 95.9 REMARK 620 4 HOH B 613 O 166.9 93.7 92.5 REMARK 620 5 HOH B 642 O 86.0 168.9 95.1 84.4 REMARK 620 6 HOH B 684 O 96.4 83.7 175.8 91.7 85.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKO B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 506 DBREF 6IND A 86 413 UNP Q08499 PDE4D_HUMAN 388 715 DBREF 6IND B 86 413 UNP Q08499 PDE4D_HUMAN 388 715 SEQADV 6IND MET A 65 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY A 66 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER A 67 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER A 68 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 69 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 70 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 71 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 72 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 73 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 74 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER A 75 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER A 76 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY A 77 UNP Q08499 EXPRESSION TAG SEQADV 6IND LEU A 78 UNP Q08499 EXPRESSION TAG SEQADV 6IND VAL A 79 UNP Q08499 EXPRESSION TAG SEQADV 6IND PRO A 80 UNP Q08499 EXPRESSION TAG SEQADV 6IND ARG A 81 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY A 82 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER A 83 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS A 84 UNP Q08499 EXPRESSION TAG SEQADV 6IND MET A 85 UNP Q08499 EXPRESSION TAG SEQADV 6IND MET B 65 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY B 66 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER B 67 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER B 68 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 69 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 70 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 71 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 72 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 73 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 74 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER B 75 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER B 76 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY B 77 UNP Q08499 EXPRESSION TAG SEQADV 6IND LEU B 78 UNP Q08499 EXPRESSION TAG SEQADV 6IND VAL B 79 UNP Q08499 EXPRESSION TAG SEQADV 6IND PRO B 80 UNP Q08499 EXPRESSION TAG SEQADV 6IND ARG B 81 UNP Q08499 EXPRESSION TAG SEQADV 6IND GLY B 82 UNP Q08499 EXPRESSION TAG SEQADV 6IND SER B 83 UNP Q08499 EXPRESSION TAG SEQADV 6IND HIS B 84 UNP Q08499 EXPRESSION TAG SEQADV 6IND 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 AKO A 501 28 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 B 501 4 HET AKO B 502 28 HET MG B 503 1 HET MG B 504 1 HET ZN B 505 1 HET EDO B 506 4 HETNAM AKO (1S)-6,7-DIMETHOXY-1-[2-(6-METHYL-1H-INDOL-3-YL)ETHYL]- HETNAM 2 AKO 3,4-DIHYDROISOQUINOLINE-2(1H)-CARBALDEHYDE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 AKO 2(C23 H26 N2 O3) FORMUL 4 MG 3(MG 2+) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 EDO 5(C2 H6 O2) FORMUL 15 HOH *320(H2 O) HELIX 1 AA1 GLU A 87 GLU A 97 1 11 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 THR A 409 1 18 HELIX 22 AC4 LEU B 92 GLU B 97 1 6 HELIX 23 AC5 ASP B 98 LYS B 101 5 4 HELIX 24 AC6 HIS B 105 SER B 113 1 9 HELIX 25 AC7 ARG B 116 ASP B 130 1 15 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 O ASP A 151 MG MG B 503 1555 3855 2.10 LINK O TYR A 153 MG MG B 503 1555 3855 2.34 LINK NE2 HIS A 164 ZN ZN A 503 1555 1555 2.20 LINK NE2 HIS A 200 ZN ZN A 503 1555 1555 2.24 LINK OD1 ASP A 201 MG MG A 502 1555 1555 2.07 LINK OD2 ASP A 201 ZN ZN A 503 1555 1555 2.14 LINK OD1 ASP A 318 ZN ZN A 503 1555 1555 2.17 LINK MG MG A 502 O HOH A 620 1555 1555 2.02 LINK MG MG A 502 O HOH A 650 1555 1555 2.17 LINK MG MG A 502 O HOH A 661 1555 1555 2.16 LINK MG MG A 502 O HOH A 685 1555 1555 2.15 LINK MG MG A 502 O HOH A 726 1555 1555 2.16 LINK ZN ZN A 503 O HOH A 620 1555 1555 2.19 LINK ZN ZN A 503 O HOH A 716 1555 1555 2.33 LINK O HOH A 707 MG MG B 503 3845 1555 2.02 LINK NE2 HIS B 164 ZN ZN B 505 1555 1555 2.22 LINK NE2 HIS B 200 ZN ZN B 505 1555 1555 2.27 LINK OD1 ASP B 201 MG MG B 504 1555 1555 2.16 LINK OD2 ASP B 201 ZN ZN B 505 1555 1555 2.07 LINK OD1 ASP B 301 MG MG B 503 1555 1555 2.29 LINK OD1 ASP B 318 ZN ZN B 505 1555 1555 2.19 LINK MG MG B 503 O HOH B 602 1555 1555 2.22 LINK MG MG B 503 O HOH B 627 1555 1555 2.21 LINK MG MG B 504 O HOH B 606 1555 1555 2.03 LINK MG MG B 504 O HOH B 607 1555 1555 2.17 LINK MG MG B 504 O HOH B 613 1555 1555 2.23 LINK MG MG B 504 O HOH B 642 1555 1555 2.19 LINK MG MG B 504 O HOH B 684 1555 1555 2.04 LINK ZN ZN B 505 O HOH B 606 1555 1555 2.20 LINK ZN ZN B 505 O HOH B 655 1555 1555 2.32 CISPEP 1 HIS A 389 PRO A 390 0 0.14 CISPEP 2 HIS B 389 PRO B 390 0 -7.11 SITE 1 AC1 9 HIS A 160 MET A 273 ASN A 321 ILE A 336 SITE 2 AC1 9 PHE A 340 MET A 357 GLN A 369 PHE A 372 SITE 3 AC1 9 HOH A 728 SITE 1 AC2 6 ASP A 201 HOH A 620 HOH A 650 HOH A 661 SITE 2 AC2 6 HOH A 685 HOH A 726 SITE 1 AC3 6 HIS A 164 HIS A 200 ASP A 201 ASP A 318 SITE 2 AC3 6 HOH A 620 HOH A 716 SITE 1 AC4 5 SER A 208 PHE A 340 PRO A 356 CYS A 358 SITE 2 AC4 5 HOH A 622 SITE 1 AC5 4 HIS A 378 PRO A 379 GLU A 382 HOH A 652 SITE 1 AC6 3 LYS A 262 ASP A 266 HOH B 616 SITE 1 AC7 5 ASN A 224 HOH A 657 LYS B 262 ILE B 265 SITE 2 AC7 5 ASP B 266 SITE 1 AC8 7 HIS B 160 MET B 273 ILE B 336 MET B 357 SITE 2 AC8 7 GLN B 369 PHE B 372 HOH B 643 SITE 1 AC9 3 ASP B 301 HOH B 602 HOH B 627 SITE 1 AD1 6 ASP B 201 HOH B 606 HOH B 607 HOH B 613 SITE 2 AD1 6 HOH B 642 HOH B 684 SITE 1 AD2 6 HIS B 164 HIS B 200 ASP B 201 ASP B 318 SITE 2 AD2 6 HOH B 606 HOH B 655 SITE 1 AD3 5 SER B 208 PHE B 340 PRO B 356 CYS B 358 SITE 2 AD3 5 HOH B 635 CRYST1 57.835 80.185 163.334 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 0.017291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006122 0.00000