HEADER TRANSCRIPTION 11-DEC-09 3L1B TITLE COMPLEX STRUCTURE OF FXR LIGAND-BINDING DOMAIN WITH A TITLE 2 TETRAHYDROAZEPINOINDOLE COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: FARNESOID X RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN, RESIDUES 248-476; COMPND 5 SYNONYM: NR1H4 PROTEIN; 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: NR1H4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEAR RECEPTOR, FXR AGONIST, FXR LIGAND-BINDING DOMAIN, NUCLEUS, KEYWDS 2 RECEPTOR, TRANSCRIPTION REGULATION, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR W.XU,J.T.LUNDQUIST REVDAT 3 03-APR-24 3L1B 1 REMARK REVDAT 2 21-FEB-24 3L1B 1 REMARK SEQADV REVDAT 1 02-MAR-10 3L1B 0 JRNL AUTH J.T.LUNDQUIST,D.C.HARNISH,C.Y.KIM,J.F.MEHLMANN,R.J.UNWALLA, JRNL AUTH 2 K.M.PHIPPS,M.L.CRAWLEY,T.COMMONS,D.M.GREEN,W.XU,W.T.HUM, JRNL AUTH 3 J.E.ETA,I.FEINGOLD,V.PATEL,M.J.EVANS,K.LAI, JRNL AUTH 4 L.BORGES-MARCUCCI,P.E.MAHANEY,J.E.WROBEL JRNL TITL IMPROVEMENT OF PHYSIOCHEMICAL PROPERTIES OF THE JRNL TITL 2 TETRAHYDROAZEPINOINDOLE SERIES OF FARNESOID X RECEPTOR (FXR) JRNL TITL 3 AGONISTS: BENEFICIAL MODULATION OF LIPIDS IN PRIMATES. JRNL REF J.MED.CHEM. V. 53 1774 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20095622 JRNL DOI 10.1021/JM901650U REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 17343 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 882 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 32.1723 - 3.4321 0.98 3069 143 0.2236 0.2268 REMARK 3 2 3.4321 - 2.7246 0.94 2783 162 0.2524 0.2622 REMARK 3 3 2.7246 - 2.3803 0.95 2748 159 0.2614 0.3266 REMARK 3 4 2.3803 - 2.1628 0.94 2741 145 0.2617 0.3461 REMARK 3 5 2.1628 - 2.0078 0.93 2687 147 0.2777 0.3114 REMARK 3 6 2.0078 - 1.9000 0.85 2433 126 0.3214 0.3834 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 : 0.37 REMARK 3 B_SOL : 57.49 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.006 1846 REMARK 3 ANGLE : 0.908 2499 REMARK 3 CHIRALITY : 0.058 273 REMARK 3 PLANARITY : 0.004 317 REMARK 3 DIHEDRAL : 16.921 690 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -5.0697 -7.6295 14.7957 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.2682 REMARK 3 T33: 0.2721 T12: -0.0177 REMARK 3 T13: -0.0074 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.5460 L22: 1.8917 REMARK 3 L33: 3.3808 L12: 0.2935 REMARK 3 L13: -0.0116 L23: -0.2020 REMARK 3 S TENSOR REMARK 3 S11: 0.0376 S12: -0.0311 S13: -0.0561 REMARK 3 S21: 0.0105 S22: -0.0032 S23: 0.1316 REMARK 3 S31: 0.0261 S32: -0.2820 S33: -0.0001 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 3L1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03800 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: IN-HOUSE FXR LIGAND-BINDING DOMAIN STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1MM HEPES, 27%PEG3350, 400MM MGCL2, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 16.92250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.28450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.68250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.28450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.92250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.68250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 244 REMARK 465 ARG A 268 REMARK 465 MET A 269 REMARK 465 PRO A 270 REMARK 465 GLN A 271 REMARK 465 GLU A 272 REMARK 465 ILE A 273 REMARK 465 THR A 274 REMARK 465 ASN A 275 REMARK 465 LYS A 276 REMARK 465 ILE A 277 REMARK 465 LEU A 278 REMARK 465 LYS A 279 REMARK 465 GLU A 280 REMARK 465 GLU A 281 REMARK 465 PHE A 282 REMARK 465 GLN A 476 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 ALA A 284 -98.09 84.40 REMARK 500 LYS A 380 64.98 26.30 REMARK 500 TYR A 401 0.68 84.69 REMARK 500 LYS A 464 150.27 51.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 635 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OSH RELATED DB: PDB REMARK 900 A CHEMICAL, GENETIC, AND STRUCTURAL ANALYSIS OF THE NUCLEAR BILE REMARK 900 ACID RECEPTOR FXR DBREF 3L1B A 248 476 UNP B7ZM06 B7ZM06_HUMAN 248 476 SEQADV 3L1B GLY A 244 UNP B7ZM06 EXPRESSION TAG SEQADV 3L1B SER A 245 UNP B7ZM06 EXPRESSION TAG SEQADV 3L1B HIS A 246 UNP B7ZM06 EXPRESSION TAG SEQADV 3L1B GLY A 247 UNP B7ZM06 EXPRESSION TAG SEQRES 1 A 233 GLY SER HIS GLY GLU LEU THR PRO ASP GLN GLN THR LEU SEQRES 2 A 233 LEU HIS PHE ILE MET ASP SER TYR ASN LYS GLN ARG MET SEQRES 3 A 233 PRO GLN GLU ILE THR ASN LYS ILE LEU LYS GLU GLU PHE SEQRES 4 A 233 SER ALA GLU GLU ASN PHE LEU ILE LEU THR GLU MET ALA SEQRES 5 A 233 THR ASN HIS VAL GLN VAL LEU VAL GLU PHE THR LYS LYS SEQRES 6 A 233 LEU PRO GLY PHE GLN THR LEU ASP HIS GLU ASP GLN ILE SEQRES 7 A 233 ALA LEU LEU LYS GLY SER ALA VAL GLU ALA MET PHE LEU SEQRES 8 A 233 ARG SER ALA GLU ILE PHE ASN LYS LYS LEU PRO SER GLY SEQRES 9 A 233 HIS SER ASP LEU LEU GLU GLU ARG ILE ARG ASN SER GLY SEQRES 10 A 233 ILE SER ASP GLU TYR ILE THR PRO MET PHE SER PHE TYR SEQRES 11 A 233 LYS SER ILE GLY GLU LEU LYS MET THR GLN GLU GLU TYR SEQRES 12 A 233 ALA LEU LEU THR ALA ILE VAL ILE LEU SER PRO ASP ARG SEQRES 13 A 233 GLN TYR ILE LYS ASP ARG GLU ALA VAL GLU LYS LEU GLN SEQRES 14 A 233 GLU PRO LEU LEU ASP VAL LEU GLN LYS LEU CYS LYS ILE SEQRES 15 A 233 HIS GLN PRO GLU ASN PRO GLN HIS PHE ALA CYS LEU LEU SEQRES 16 A 233 GLY ARG LEU THR GLU LEU ARG THR PHE ASN HIS HIS HIS SEQRES 17 A 233 ALA GLU MET LEU MET SER TRP ARG VAL ASN ASP HIS LYS SEQRES 18 A 233 PHE THR PRO LEU LEU CYS GLU ILE TRP ASP VAL GLN HET 635 A 1 41 HETNAM 635 1-METHYLETHYL 8-FLUORO-1,1-DIMETHYL-3-{[4-(3-MORPHOLIN- HETNAM 2 635 4-YLPROPOXY)PHENYL]CARBONYL}-1,2,3,6- HETNAM 3 635 TETRAHYDROAZEPINO[4,5-B]INDOLE-5-CARBOXYLATE FORMUL 2 635 C32 H38 F N3 O5 FORMUL 3 HOH *30(H2 O) HELIX 1 1 SER A 245 LEU A 249 5 5 HELIX 2 2 THR A 250 ASN A 265 1 16 HELIX 3 3 ALA A 284 LEU A 309 1 26 HELIX 4 4 GLY A 311 LEU A 315 5 5 HELIX 5 5 ASP A 316 LYS A 343 1 28 HELIX 6 6 PRO A 345 GLY A 347 5 3 HELIX 7 7 HIS A 348 ASN A 358 1 11 HELIX 8 8 SER A 362 LEU A 379 1 18 HELIX 9 9 THR A 382 LEU A 395 1 14 HELIX 10 10 ASP A 404 GLN A 427 1 24 HELIX 11 11 GLN A 432 THR A 446 1 15 HELIX 12 12 THR A 446 ASN A 461 1 16 HELIX 13 13 THR A 466 TRP A 473 1 8 SITE 1 AC1 14 PHE A 288 LEU A 291 THR A 292 MET A 294 SITE 2 AC1 14 ALA A 295 MET A 332 SER A 336 ILE A 339 SITE 3 AC1 14 LYS A 343 LEU A 352 ILE A 356 TYR A 373 SITE 4 AC1 14 TRP A 458 TRP A 473 CRYST1 33.845 55.365 118.569 90.00 90.00 90.00 P 21 21 21 4 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 0.029546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008434 0.00000