PDB Short entry for 1JP1 HEADER HYDROLASE 31-JUL-01 1JP1 TITLE MOLECULAR DOCKING OF COMPETITIVE PHOSPHODIESTERASE TITLE 2 SUBSTRATE CYCLIC ADENOSINE 3',5'-MONOPHOSPHATE (CAMP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHODIESTERASE 4B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDE4B; COMPND 5 EC: 3.1.4.17; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS CAMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE EXPDTA THEORETICAL MODEL AUTHOR O.DYM,I.XENARIOS,H.KE,J.COLICELLI REVDAT 2 16-JAN-02 1JP1 1 JRNL REVDAT 1 15-AUG-01 1JP1 0 JRNL AUTH O.DYM,I.XENARIOS,H.KE,J.COLICELLI JRNL TITL MOLECULAR DOCKING OF COMPETITIVE PHOSPHODIESTERASE JRNL TITL 2 INHIBITORS. JRNL REF MOL.PHARMACOL. V. 61 20 2002 JRNL REFN ASTM MOPMA3 US ISSN 0026-895X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JP1 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-2001. REMARK 100 THE RCSB ID CODE IS RCSB014019. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: AUTOMATED DOCKING SIMULATION, USING AUTODOCK PROGRAM, REMARK 220 WAS IMPLEMENTED TO DOCK CAMP (1NHK) INTO THE ACTIVE SITE REMARK 220 OF PDE4 (1F0J). THE SIMULATIONS WERE COMPOSED OF 100 REMARK 220 DOCKING RUNS, EACH OF 50 CYCLES CONTAINING A MAXIMUM OF REMARK 220 10,000 ACCEPTED AND REJECTED STEPS. THE SIMULATED REMARK 220 ANNEALING PROCEDURE WAS STARTED AT HIGH TEMPERATURE (RT= REMARK 220 616KCAL.MOL) AND WAS DECREASED BY A FACTOR OF 0.95 ON REMARK 220 EACH CYCLE. THE 100 DOCKED COMPLEXES WERE CLUSTERED WITH REMARK 220 RMSD TOLERANCE OF 1ANG. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 490 REMARK 465 PRO A 491 REMARK 465 LEU A 492 REMARK 465 ASP A 493 REMARK 465 GLU A 494 REMARK 465 GLN A 495 REMARK 465 GLU A 509 REMARK 465 LEU A 510 REMARK 465 THR A 511 REMARK 465 LEU A 512 REMARK 465 ASP A 513 REMARK 465 GLU A 514 REMARK 465 GLU A 515 REMARK 465 ASP A 516 REMARK 465 SER A 517 REMARK 465 GLU A 518 REMARK 465 GLY A 519 REMARK 465 PRO A 520 REMARK 465 GLU A 521 REMARK 465 LYS A 522 REMARK 465 GLU A 523 REMARK 465 GLY A 524 REMARK 465 GLU A 525 REMARK 465 GLY A 526 REMARK 465 HIS A 527 REMARK 465 SER A 528 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 196 SD MET A 196 CE 0.087 REMARK 500 MET A 296 SD MET A 296 CE 0.051 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 227 N - CA - C ANGL. DEV. =-10.1 DEGREES REMARK 500 VAL A 231 N - CA - C ANGL. DEV. =-10.5 DEGREES REMARK 500 ALA A 232 N - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 HIS A 274 N - CA - C ANGL. DEV. = 11.1 DEGREES REMARK 500 LEU A 326 CA - CB - CG ANGL. DEV. = 9.2 DEGREES REMARK 500 SER A 438 N - CA - C ANGL. DEV. = -8.0 DEGREES REMARK 500 TYR A 449 N - CA - C ANGL. DEV. = 8.1 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F0J RELATED DB: PDB REMARK 900 CAMP WAS DOCKED INTO CHAIN A OF THIS COORDINATE SET. REMARK 900 RELATED ID: 1NHK RELATED DB: PDB REMARK 900 CAMP OF THIS COORDINATE SET WAS DOCKED INTO CHAIN A OF 1F0J. DBREF 1JP1 A 152 528 UNP Q07343 CN4B_HUMAN 324 700 SEQADV 1JP1 ALA A 487 UNP Q07343 SER 659 ENGINEERED SEQADV 1JP1 ALA A 489 UNP Q07343 SER 661 ENGINEERED SEQRES 1 A 377 SER ILE SER ARG PHE GLY VAL ASN THR GLU ASN GLU ASP SEQRES 2 A 377 HIS LEU ALA LYS GLU LEU GLU ASP LEU ASN LYS TRP GLY SEQRES 3 A 377 LEU ASN ILE PHE ASN VAL ALA GLY TYR SER HIS ASN ARG SEQRES 4 A 377 PRO LEU THR CYS ILE MET TYR ALA ILE PHE GLN GLU ARG SEQRES 5 A 377 ASP LEU LEU LYS THR PHE ARG ILE SER SER ASP THR PHE SEQRES 6 A 377 ILE THR TYR MET MET THR LEU GLU ASP HIS TYR HIS SER SEQRES 7 A 377 ASP VAL ALA TYR HIS ASN SER LEU HIS ALA ALA ASP VAL SEQRES 8 A 377 ALA GLN SER THR HIS VAL LEU LEU SER THR PRO ALA LEU SEQRES 9 A 377 ASP ALA VAL PHE THR ASP LEU GLU ILE LEU ALA ALA ILE SEQRES 10 A 377 PHE ALA ALA ALA ILE HIS ASP VAL ASP HIS PRO GLY VAL SEQRES 11 A 377 SER ASN GLN PHE LEU ILE ASN THR ASN SER GLU LEU ALA SEQRES 12 A 377 LEU MET TYR ASN ASP GLU SER VAL LEU GLU ASN HIS HIS SEQRES 13 A 377 LEU ALA VAL GLY PHE LYS LEU LEU GLN GLU GLU HIS CYS SEQRES 14 A 377 ASP ILE PHE MET ASN LEU THR LYS LYS GLN ARG GLN THR SEQRES 15 A 377 LEU ARG LYS MET VAL ILE ASP MET VAL LEU ALA THR ASP SEQRES 16 A 377 MET SER LYS HIS MET SER LEU LEU ALA ASP LEU LYS THR SEQRES 17 A 377 MET VAL GLU THR LYS LYS VAL THR SER SER GLY VAL LEU SEQRES 18 A 377 LEU LEU ASP ASN TYR THR ASP ARG ILE GLN VAL LEU ARG SEQRES 19 A 377 ASN MET VAL HIS CYS ALA ASP LEU SER ASN PRO THR LYS SEQRES 20 A 377 SER LEU GLU LEU TYR ARG GLN TRP THR ASP ARG ILE MET SEQRES 21 A 377 GLU GLU PHE PHE GLN GLN GLY ASP LYS GLU ARG GLU ARG SEQRES 22 A 377 GLY MET GLU ILE SER PRO MET CYS ASP LYS HIS THR ALA SEQRES 23 A 377 SER VAL GLU LYS SER GLN VAL GLY PHE ILE ASP TYR ILE SEQRES 24 A 377 VAL HIS PRO LEU TRP GLU THR TRP ALA ASP LEU VAL GLN SEQRES 25 A 377 PRO ASP ALA GLN ASP ILE LEU ASP THR LEU GLU ASP ASN SEQRES 26 A 377 ARG ASN TRP TYR GLN SER MET ILE PRO GLN ALA PRO ALA SEQRES 27 A 377 PRO PRO LEU ASP GLU GLN ASN ARG ASP CYS GLN GLY LEU SEQRES 28 A 377 MET GLU LYS PHE GLN PHE GLU LEU THR LEU ASP GLU GLU SEQRES 29 A 377 ASP SER GLU GLY PRO GLU LYS GLU GLY GLU GLY HIS SER HET CMP 700 25 HETNAM CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE HETSYN CMP CYCLIC AMP; CAMP FORMUL 2 CMP C10 H12 N5 O6 P HELIX 1 1 ASN A 159 LEU A 170 1 12 HELIX 2 2 GLU A 171 LEU A 173 5 3 HELIX 3 3 ASN A 179 SER A 187 1 9 HELIX 4 4 ARG A 190 ARG A 203 1 14 HELIX 5 5 ASP A 204 PHE A 209 1 6 HELIX 6 6 SER A 212 HIS A 226 1 15 HELIX 7 7 ASN A 235 SER A 251 1 17 HELIX 8 8 THR A 252 ASP A 256 5 5 HELIX 9 9 THR A 260 HIS A 274 1 15 HELIX 10 10 SER A 282 THR A 289 1 8 HELIX 11 11 SER A 291 TYR A 297 1 7 HELIX 12 12 SER A 301 LEU A 314 1 14 HELIX 13 13 LEU A 315 GLU A 317 5 3 HELIX 14 14 THR A 327 ALA A 344 1 18 HELIX 15 15 THR A 345 SER A 348 5 4 HELIX 16 16 LYS A 349 LYS A 364 1 16 HELIX 17 17 ASN A 376 LEU A 393 1 18 HELIX 18 18 SER A 394 LYS A 398 5 5 HELIX 19 19 SER A 399 ARG A 424 1 26 HELIX 20 20 SER A 438 ILE A 450 1 13 HELIX 21 21 ILE A 450 GLN A 463 1 14 HELIX 22 22 ALA A 466 MET A 483 1 18 HELIX 23 23 ASP A 498 PHE A 506 1 9 CISPEP 1 GLN A 463 PRO A 464 0 -0.64 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000