PDB Short entry for 1Y5D HEADER SIGNALING PROTEIN 02-DEC-04 1Y5D TITLE HOMOLOGY MODEL OF THE TRANSMEMBRANE REGIONS OF CCR1 SHOWING TITLE 2 PROPOSED BINDING SITE FOR THE CHEMOKINE RECEPTOR TITLE 3 ANTAGONIST UCB 35625 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C CHEMOKINE RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-C CKR-1, CC-CKR-1, CCR-1, CCR1, MACROPHAGE COMPND 5 INFLAMMATORY PROTEIN-1 ALPHA RECEPTOR, MIP-1ALPHA-R, COMPND 6 RANTES-R, HM145, LD78 RECEPTOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN KEYWDS COMPUTATIONAL MODEL, DOCKING, CCR1, UCB 35625, KEYWDS 2 TRANSMEMBRANE REGIONS EXPDTA THEORETICAL MODEL AUTHOR F.L.DE MENDONCA,P.C.DA FONSECA,R.M.PHILLIPS,J.W.SALDANHA, AUTHOR 2 T.J.WILLIAMS,J.E.PEASE REVDAT 2 17-JAN-06 1Y5D 1 JRNL REVDAT 1 11-JAN-05 1Y5D 0 JRNL AUTH F.L.DE MENDONCA,P.C.DA FONSECA,R.M.PHILLIPS, JRNL AUTH 2 J.W.SALDANHA,T.J.WILLIAMS,J.E.PEASE JRNL TITL SITE-DIRECTED MUTAGENESIS OF CC CHEMOKINE RECEPTOR JRNL TITL 2 1 REVEALS THE MECHANISM OF ACTION OF UCB 35625, A JRNL TITL 3 SMALL MOLECULE CHEMOKINE RECEPTOR ANTAGONIST JRNL REF J.BIOL.CHEM. V. 280 4808 2005 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.SABROE,M.J.PECK,B.J.VAN KEULEN,A.JORRITSMA, REMARK 1 AUTH 2 G.SIMMONS,P.R.CLAPHAM,T.J.WILLIAMS,J.E.PEASE REMARK 1 TITL A SMALL MOLECULE ANTAGONIST OF CHEMOKINE RECEPTORS REMARK 1 TITL 2 CCR1 AND CCR3. POTENT INHIBITION OF EOSINOPHIL REMARK 1 TITL 3 FUNCTION AND CCR3-MEDIATED HIV-1 ENTRY REMARK 1 REF J.BIOL.CHEM. V. 275 25985 2000 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.NAYA,Y.SAGARA,K.OHWAKI,T.SAEKI,D.ICHIKAWA, REMARK 1 AUTH 2 Y.IWASAWA,K.NOGUCHI,N.OHTAKE REMARK 1 TITL DESIGN, SYNTHESIS, AND DISCOVERY OF A NOVEL CCR1 REMARK 1 TITL 2 ANTAGONIST REMARK 1 REF J.MED.CHEM. V. 44 1429 2001 REMARK 1 REFN ASTM JMCMAR US ISSN 0022-2623 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DEEPVIEW/SWISS-PDBVIEWER 3.7 REMARK 3 AUTHORS : GUEX, N., PEITSCH, M, SCHWEDE, T., DIEMAND, A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y5D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-2004. REMARK 100 THE RCSB ID CODE IS RCSB031136. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: COMPUTATIONAL HOMOLOGY MODELLING AND MANUAL LIGAND REMARK 220 DOCKING. THE COMPUTER MODEL OF THE TRANSMEMBRANE REGIONS REMARK 220 OF THE HUMAN CCR1 RECEPTOR WAS BUILT, BASED ON THE REMARK 220 STRUCTURE OF BOVINE RHODOPSIN (PDB, 1F88) AS TEMPLATE, REMARK 220 USING THE PROGRAM DEEPVIEW/SWISS-PDBVIEWER (HTTP:// REMARK 220 CA.EXPASY.ORG/SPDBV/). THIS PROGRAM WAS ALSO USED FOR REMARK 220 THE MANUAL DOCKING OF UCB 35625 TO THE RECEPTOR, USING REMARK 220 INFORMATION PROVIDED BY MOLECULAR BIOLOGY EXPERIMENTS. REMARK 220 ENERGY MINIMISATION WAS PERFORMED USING THE GROMOS96 REMARK 220 IMPLEMENTATION OF SWISS-PDBVIEWER. THE STRUCTURE OF UCB REMARK 220 35625 WAS BUILT USING THE PROGRAM CHEMDRAW PRO 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 THR A 6 REMARK 465 THR A 7 REMARK 465 GLU A 8 REMARK 465 ASP A 9 REMARK 465 TYR A 10 REMARK 465 ASP A 11 REMARK 465 THR A 12 REMARK 465 THR A 13 REMARK 465 THR A 14 REMARK 465 GLU A 15 REMARK 465 PHE A 16 REMARK 465 ASP A 17 REMARK 465 TYR A 18 REMARK 465 GLY A 19 REMARK 465 ASP A 20 REMARK 465 ALA A 21 REMARK 465 THR A 22 REMARK 465 PRO A 23 REMARK 465 CYS A 24 REMARK 465 GLN A 25 REMARK 465 LYS A 26 REMARK 465 VAL A 27 REMARK 465 ASN A 28 REMARK 465 GLU A 29 REMARK 465 ARG A 30 REMARK 465 ALA A 31 REMARK 465 PHE A 32 REMARK 465 GLY A 33 REMARK 465 ALA A 34 REMARK 465 GLN A 35 REMARK 465 LEU A 36 REMARK 465 TYR A 62 REMARK 465 LYS A 63 REMARK 465 ARG A 64 REMARK 465 LEU A 65 REMARK 465 LYS A 66 REMARK 465 ASN A 67 REMARK 465 MET A 68 REMARK 465 LYS A 94 REMARK 465 LEU A 95 REMARK 465 LYS A 96 REMARK 465 ASP A 97 REMARK 465 ASP A 98 REMARK 465 TRP A 99 REMARK 465 VAL A 100 REMARK 465 PHE A 101 REMARK 465 GLY A 102 REMARK 465 ASP A 103 REMARK 465 ALA A 104 REMARK 465 MET A 105 REMARK 465 CYS A 106 REMARK 465 LYS A 107 REMARK 465 ARG A 131 REMARK 465 TYR A 132 REMARK 465 LEU A 133 REMARK 465 ALA A 134 REMARK 465 ILE A 135 REMARK 465 VAL A 136 REMARK 465 HIS A 137 REMARK 465 ALA A 138 REMARK 465 VAL A 139 REMARK 465 PHE A 140 REMARK 465 ALA A 141 REMARK 465 LEU A 142 REMARK 465 ARG A 143 REMARK 465 ALA A 144 REMARK 465 ARG A 145 REMARK 465 THR A 146 REMARK 465 TYR A 170 REMARK 465 PHE A 171 REMARK 465 SER A 172 REMARK 465 LYS A 173 REMARK 465 THR A 174 REMARK 465 GLN A 175 REMARK 465 TRP A 176 REMARK 465 GLU A 177 REMARK 465 PHE A 178 REMARK 465 THR A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 THR A 182 REMARK 465 CYS A 183 REMARK 465 SER A 184 REMARK 465 LEU A 185 REMARK 465 HIS A 186 REMARK 465 PHE A 187 REMARK 465 PRO A 188 REMARK 465 HIS A 189 REMARK 465 GLU A 190 REMARK 465 SER A 191 REMARK 465 LEU A 192 REMARK 465 ARG A 193 REMARK 465 GLU A 194 REMARK 465 TRP A 195 REMARK 465 GLY A 221 REMARK 465 ILE A 222 REMARK 465 ILE A 223 REMARK 465 LYS A 224 REMARK 465 ILE A 225 REMARK 465 LEU A 226 REMARK 465 LEU A 227 REMARK 465 ARG A 228 REMARK 465 ARG A 229 REMARK 465 PRO A 230 REMARK 465 ASN A 231 REMARK 465 GLU A 232 REMARK 465 LYS A 233 REMARK 465 LYS A 234 REMARK 465 SER A 235 REMARK 465 SER A 262 REMARK 465 VAL A 263 REMARK 465 PHE A 264 REMARK 465 GLN A 265 REMARK 465 ASP A 266 REMARK 465 PHE A 267 REMARK 465 LEU A 268 REMARK 465 PHE A 269 REMARK 465 THR A 270 REMARK 465 HIS A 271 REMARK 465 GLU A 272 REMARK 465 CYS A 273 REMARK 465 GLU A 274 REMARK 465 GLN A 275 REMARK 465 SER A 276 REMARK 465 ARG A 277 REMARK 465 HIS A 278 REMARK 465 LEU A 279 REMARK 465 PHE A 303 REMARK 465 VAL A 304 REMARK 465 GLY A 305 REMARK 465 GLU A 306 REMARK 465 ARG A 307 REMARK 465 PHE A 308 REMARK 465 ARG A 309 REMARK 465 LYS A 310 REMARK 465 TYR A 311 REMARK 465 LEU A 312 REMARK 465 ARG A 313 REMARK 465 GLN A 314 REMARK 465 LEU A 315 REMARK 465 PHE A 316 REMARK 465 HIS A 317 REMARK 465 ARG A 318 REMARK 465 ARG A 319 REMARK 465 VAL A 320 REMARK 465 ALA A 321 REMARK 465 VAL A 322 REMARK 465 HIS A 323 REMARK 465 LEU A 324 REMARK 465 VAL A 325 REMARK 465 LYS A 326 REMARK 465 TRP A 327 REMARK 465 LEU A 328 REMARK 465 PRO A 329 REMARK 465 PHE A 330 REMARK 465 LEU A 331 REMARK 465 SER A 332 REMARK 465 VAL A 333 REMARK 465 ASP A 334 REMARK 465 ARG A 335 REMARK 465 LEU A 336 REMARK 465 GLU A 337 REMARK 465 ARG A 338 REMARK 465 VAL A 339 REMARK 465 SER A 340 REMARK 465 SER A 341 REMARK 465 THR A 342 REMARK 465 SER A 343 REMARK 465 PRO A 344 REMARK 465 SER A 345 REMARK 465 THR A 346 REMARK 465 GLY A 347 REMARK 465 GLU A 348 REMARK 465 HIS A 349 REMARK 465 GLU A 350 REMARK 465 LEU A 351 REMARK 465 SER A 352 REMARK 465 ALA A 353 REMARK 465 GLY A 354 REMARK 465 PHE A 355 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 41 CB - CG - CD2 ANGL. DEV. =-14.0 DEGREES REMARK 500 ILE A 108 CB - CA - C ANGL. DEV. = 16.0 DEGREES REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINED METHOD: AUTHOR DETERMINED DBREF 1Y5D A 1 355 UNP P32246 CKR1_HUMAN 1 355 SEQRES 1 A 355 MET GLU THR PRO ASN THR THR GLU ASP TYR ASP THR THR SEQRES 2 A 355 THR GLU PHE ASP TYR GLY ASP ALA THR PRO CYS GLN LYS SEQRES 3 A 355 VAL ASN GLU ARG ALA PHE GLY ALA GLN LEU LEU PRO PRO SEQRES 4 A 355 LEU TYR SER LEU VAL PHE VAL ILE GLY LEU VAL GLY ASN SEQRES 5 A 355 ILE LEU VAL VAL LEU VAL LEU VAL GLN TYR LYS ARG LEU SEQRES 6 A 355 LYS ASN MET THR SER ILE TYR LEU LEU ASN LEU ALA ILE SEQRES 7 A 355 SER ASP LEU LEU PHE LEU PHE THR LEU PRO PHE TRP ILE SEQRES 8 A 355 ASP TYR LYS LEU LYS ASP ASP TRP VAL PHE GLY ASP ALA SEQRES 9 A 355 MET CYS LYS ILE LEU SER GLY PHE TYR TYR THR GLY LEU SEQRES 10 A 355 TYR SER GLU ILE PHE PHE ILE ILE LEU LEU THR ILE ASP SEQRES 11 A 355 ARG TYR LEU ALA ILE VAL HIS ALA VAL PHE ALA LEU ARG SEQRES 12 A 355 ALA ARG THR VAL THR PHE GLY VAL ILE THR SER ILE ILE SEQRES 13 A 355 ILE TRP ALA LEU ALA ILE LEU ALA SER MET PRO GLY LEU SEQRES 14 A 355 TYR PHE SER LYS THR GLN TRP GLU PHE THR HIS HIS THR SEQRES 15 A 355 CYS SER LEU HIS PHE PRO HIS GLU SER LEU ARG GLU TRP SEQRES 16 A 355 LYS LEU PHE GLN ALA LEU LYS LEU ASN LEU PHE GLY LEU SEQRES 17 A 355 VAL LEU PRO LEU LEU VAL MET ILE ILE CYS TYR THR GLY SEQRES 18 A 355 ILE ILE LYS ILE LEU LEU ARG ARG PRO ASN GLU LYS LYS SEQRES 19 A 355 SER LYS ALA VAL ARG LEU ILE PHE VAL ILE MET ILE ILE SEQRES 20 A 355 PHE PHE LEU PHE TRP THR PRO TYR ASN LEU THR ILE LEU SEQRES 21 A 355 ILE SER VAL PHE GLN ASP PHE LEU PHE THR HIS GLU CYS SEQRES 22 A 355 GLU GLN SER ARG HIS LEU ASP LEU ALA VAL GLN VAL THR SEQRES 23 A 355 GLU VAL ILE ALA TYR THR HIS CYS CYS VAL ASN PRO VAL SEQRES 24 A 355 ILE TYR ALA PHE VAL GLY GLU ARG PHE ARG LYS TYR LEU SEQRES 25 A 355 ARG GLN LEU PHE HIS ARG ARG VAL ALA VAL HIS LEU VAL SEQRES 26 A 355 LYS TRP LEU PRO PHE LEU SER VAL ASP ARG LEU GLU ARG SEQRES 27 A 355 VAL SER SER THR SER PRO SER THR GLY GLU HIS GLU LEU SEQRES 28 A 355 SER ALA GLY PHE HET UCB 1000 72 HETNAM UCB 1-(CYCLOHEPTYLMETHYL)-4-{[(2,7-DICHLORO-9H-XANTHEN-9- HETNAM 2 UCB YL)CARBONYL]AMINO}-1-ETHYLPIPERIDINIUM HETSYN UCB UCB35625 FORMUL 2 UCB C29 H37 CL2 N2 O2 1+ HELIX 1 1 LEU A 37 GLN A 61 1 25 HELIX 2 2 THR A 69 TYR A 93 1 25 HELIX 3 3 ILE A 108 ASP A 130 1 23 HELIX 4 4 VAL A 147 LEU A 169 1 23 HELIX 5 5 LEU A 197 THR A 220 1 24 HELIX 6 6 LYS A 236 ILE A 261 1 26 HELIX 7 7 ASP A 280 ALA A 302 1 23 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