HEADER LIPID BINDING PROTEIN 17-JUL-17 5Y0F TITLE CRYSTAL STRUCTURE OF HUMAN FABP4 COMPLEXED WITH LIGAND 2-FLUORO-5-((4- TITLE 2 METHOXYNAPHTHALENE)-1-SULFONAMIDO) BENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, ADIPOCYTE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADIPOCYTE LIPID-BINDING PROTEIN,ALBP,ADIPOCYTE-TYPE FATTY COMPND 5 ACID-BINDING PROTEIN,AFABP,FATTY ACID-BINDING PROTEIN 4; 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: FABP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS LIPID BINDING PROTEIN, FABP4, INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR H.X.SU,Q.F.LIU,Y.C.XU REVDAT 2 27-MAR-24 5Y0F 1 REMARK REVDAT 1 06-JUN-18 5Y0F 0 JRNL AUTH D.D.GAO,H.X.DOU,H.X.SU,M.M.ZHANG,T.WANG,Q.F.LIU,H.Y.CAI, JRNL AUTH 2 H.P.DING,Z.YANG,W.L.ZHU,Y.C.XU,H.Y.WANG,Y.X.LI JRNL TITL FROM HIT TO LEAD: STRUCTURE-BASED DISCOVERY OF JRNL TITL 2 NAPHTHALENE-1-SULFONAMIDE DERIVATIVES AS POTENT AND JRNL TITL 3 SELECTIVE INHIBITORS OF FATTY ACID BINDING PROTEIN 4 JRNL REF EUR J MED CHEM V. 154 44 2018 JRNL REFN ISSN 1768-3254 JRNL PMID 29775936 JRNL DOI 10.1016/J.EJMECH.2018.05.007 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 36690 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1104 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 43.7233 - 3.0859 0.99 4485 139 0.1576 0.1730 REMARK 3 2 3.0859 - 2.4494 1.00 4473 143 0.1871 0.1601 REMARK 3 3 2.4494 - 2.1398 0.99 4512 138 0.1726 0.1861 REMARK 3 4 2.1398 - 1.9441 0.99 4485 138 0.1667 0.1848 REMARK 3 5 1.9441 - 1.8048 1.00 4508 136 0.1728 0.1737 REMARK 3 6 1.8048 - 1.6984 0.99 4487 140 0.1825 0.2627 REMARK 3 7 1.6984 - 1.6133 1.00 4486 137 0.1983 0.2153 REMARK 3 8 1.6133 - 1.5431 0.91 4150 133 0.2069 0.2333 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.860 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 1100 REMARK 3 ANGLE : 0.715 1483 REMARK 3 CHIRALITY : 0.054 168 REMARK 3 PLANARITY : 0.004 185 REMARK 3 DIHEDRAL : 2.769 923 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 5Y0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36692 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 43.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.340 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.280 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 (%): 36.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TRISODIUM CITRATE, PH6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 16.18500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.62500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.62500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.18500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.84500 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 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 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 ARG A -4 CG CD NE CZ NH1 NH2 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 O HOH A 388 O HOH A 415 2.15 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 ASP A 77 31.75 72.53 REMARK 500 ASP A 110 -131.99 51.05 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 8JO A 200 DBREF 5Y0F A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 5Y0F MET A -20 UNP P15090 EXPRESSION TAG SEQADV 5Y0F GLY A -19 UNP P15090 EXPRESSION TAG SEQADV 5Y0F SER A -18 UNP P15090 EXPRESSION TAG SEQADV 5Y0F SER A -17 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -16 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -15 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -14 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -13 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -12 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -11 UNP P15090 EXPRESSION TAG SEQADV 5Y0F SER A -10 UNP P15090 EXPRESSION TAG SEQADV 5Y0F SER A -9 UNP P15090 EXPRESSION TAG SEQADV 5Y0F GLY A -8 UNP P15090 EXPRESSION TAG SEQADV 5Y0F LEU A -7 UNP P15090 EXPRESSION TAG SEQADV 5Y0F VAL A -6 UNP P15090 EXPRESSION TAG SEQADV 5Y0F PRO A -5 UNP P15090 EXPRESSION TAG SEQADV 5Y0F ARG A -4 UNP P15090 EXPRESSION TAG SEQADV 5Y0F GLY A -3 UNP P15090 EXPRESSION TAG SEQADV 5Y0F SER A -2 UNP P15090 EXPRESSION TAG SEQADV 5Y0F HIS A -1 UNP P15090 EXPRESSION TAG SEQRES 1 A 152 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 152 LEU VAL PRO ARG GLY SER HIS MET CYS ASP ALA PHE VAL SEQRES 3 A 152 GLY THR TRP LYS LEU VAL SER SER GLU ASN PHE ASP ASP SEQRES 4 A 152 TYR MET LYS GLU VAL GLY VAL GLY PHE ALA THR ARG LYS SEQRES 5 A 152 VAL ALA GLY MET ALA LYS PRO ASN MET ILE ILE SER VAL SEQRES 6 A 152 ASN GLY ASP VAL ILE THR ILE LYS SER GLU SER THR PHE SEQRES 7 A 152 LYS ASN THR GLU ILE SER PHE ILE LEU GLY GLN GLU PHE SEQRES 8 A 152 ASP GLU VAL THR ALA ASP ASP ARG LYS VAL LYS SER THR SEQRES 9 A 152 ILE THR LEU ASP GLY GLY VAL LEU VAL HIS VAL GLN LYS SEQRES 10 A 152 TRP ASP GLY LYS SER THR THR ILE LYS ARG LYS ARG GLU SEQRES 11 A 152 ASP ASP LYS LEU VAL VAL GLU CYS VAL MET LYS GLY VAL SEQRES 12 A 152 THR SER THR ARG VAL TYR GLU ARG ALA HET 8JO A 200 26 HETNAM 8JO 2-FLUORANYL-5-[(4-METHOXYNAPHTHALEN-1-YL) HETNAM 2 8JO SULFONYLAMINO]BENZOIC ACID FORMUL 2 8JO C18 H14 F N O5 S FORMUL 3 HOH *115(H2 O) HELIX 1 AA1 HIS A -1 VAL A 5 5 7 HELIX 2 AA2 ASN A 15 GLY A 24 1 10 HELIX 3 AA3 GLY A 26 ALA A 36 1 11 SHEET 1 AA110 ASN A 59 ILE A 65 0 SHEET 2 AA110 VAL A 48 GLU A 54 -1 N ILE A 49 O PHE A 64 SHEET 3 AA110 ASN A 39 ASN A 45 -1 N ILE A 41 O LYS A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O MET A 40 SHEET 5 AA110 VAL A 122 ARG A 130 -1 O VAL A 127 N VAL A 11 SHEET 6 AA110 LYS A 112 MET A 119 -1 N VAL A 115 O ARG A 126 SHEET 7 AA110 LYS A 100 GLU A 109 -1 N LYS A 105 O GLU A 116 SHEET 8 AA110 VAL A 90 TRP A 97 -1 N TRP A 97 O LYS A 100 SHEET 9 AA110 LYS A 79 ASP A 87 -1 N THR A 85 O VAL A 92 SHEET 10 AA110 PHE A 70 VAL A 73 -1 N GLU A 72 O VAL A 80 SITE 1 AC1 18 PHE A 16 MET A 20 ALA A 33 THR A 74 SITE 2 AC1 18 ALA A 75 ASP A 76 ARG A 78 GLN A 95 SITE 3 AC1 18 ILE A 104 VAL A 115 CYS A 117 ARG A 126 SITE 4 AC1 18 TYR A 128 HOH A 313 HOH A 319 HOH A 329 SITE 5 AC1 18 HOH A 356 HOH A 365 CRYST1 32.370 53.690 75.250 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 0.030893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013289 0.00000