HEADER LIPID BINDING PROTEIN 19-JUL-17 5Y13 TITLE CRYSTAL STRUCTURE OF HUMAN FABP4 COMPLEXED WITH LIGAND 5-((4- TITLE 2 BROMONAPHTHALENE)-1-SULFONAMIDO)PENTANOIC 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(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) 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 5Y13 1 REMARK REVDAT 1 06-JUN-18 5Y13 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. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 25251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2530 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 29.9943 - 4.5814 0.80 1031 114 0.1911 0.2477 REMARK 3 2 4.5814 - 3.6384 0.92 1170 128 0.1582 0.1554 REMARK 3 3 3.6384 - 3.1791 0.98 1283 142 0.1587 0.1877 REMARK 3 4 3.1791 - 2.8887 1.00 1300 138 0.1818 0.2362 REMARK 3 5 2.8887 - 2.6817 1.00 1287 147 0.2099 0.2768 REMARK 3 6 2.6817 - 2.5237 1.00 1272 140 0.1990 0.2364 REMARK 3 7 2.5237 - 2.3974 1.00 1304 146 0.1818 0.2047 REMARK 3 8 2.3974 - 2.2931 1.00 1296 143 0.1767 0.2297 REMARK 3 9 2.2931 - 2.2048 1.00 1273 147 0.1751 0.2182 REMARK 3 10 2.2048 - 2.1288 1.00 1303 146 0.1706 0.2272 REMARK 3 11 2.1288 - 2.0622 1.00 1274 139 0.1696 0.2254 REMARK 3 12 2.0622 - 2.0033 1.00 1294 144 0.1634 0.2515 REMARK 3 13 2.0033 - 1.9505 1.00 1299 145 0.1670 0.2141 REMARK 3 14 1.9505 - 1.9030 1.00 1259 144 0.1695 0.2120 REMARK 3 15 1.9030 - 1.8597 1.00 1307 145 0.1749 0.2172 REMARK 3 16 1.8597 - 1.8201 1.00 1271 139 0.1678 0.2374 REMARK 3 17 1.8201 - 1.7837 1.00 1319 146 0.1689 0.2510 REMARK 3 18 1.7837 - 1.7501 0.95 1179 137 0.1693 0.2250 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.39 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 1094 REMARK 3 ANGLE : 1.075 1473 REMARK 3 CHIRALITY : 0.067 168 REMARK 3 PLANARITY : 0.003 184 REMARK 3 DIHEDRAL : 14.742 412 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 5Y13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 29.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.655 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.48 REMARK 200 R MERGE FOR SHELL (I) : 0.07300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.64 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 (%): 37.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TRISODIUM CITRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 16.34500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.68000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.82000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.68000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.82000 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 470 HIS A -1 CG ND1 CD2 CE1 NE2 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 OE1 GLU A 129 O HOH A 301 2.09 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 110 -126.40 51.02 REMARK 500 LYS A 120 -114.94 57.16 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 8K0 A 201 DBREF 5Y13 A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 5Y13 MET A -20 UNP P15090 EXPRESSION TAG SEQADV 5Y13 GLY A -19 UNP P15090 EXPRESSION TAG SEQADV 5Y13 SER A -18 UNP P15090 EXPRESSION TAG SEQADV 5Y13 SER A -17 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -16 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -15 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -14 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -13 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -12 UNP P15090 EXPRESSION TAG SEQADV 5Y13 HIS A -11 UNP P15090 EXPRESSION TAG SEQADV 5Y13 SER A -10 UNP P15090 EXPRESSION TAG SEQADV 5Y13 SER A -9 UNP P15090 EXPRESSION TAG SEQADV 5Y13 GLY A -8 UNP P15090 EXPRESSION TAG SEQADV 5Y13 LEU A -7 UNP P15090 EXPRESSION TAG SEQADV 5Y13 VAL A -6 UNP P15090 EXPRESSION TAG SEQADV 5Y13 PRO A -5 UNP P15090 EXPRESSION TAG SEQADV 5Y13 ARG A -4 UNP P15090 EXPRESSION TAG SEQADV 5Y13 GLY A -3 UNP P15090 EXPRESSION TAG SEQADV 5Y13 SER A -2 UNP P15090 EXPRESSION TAG SEQADV 5Y13 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 8K0 A 201 22 HETNAM 8K0 5-[(4-BROMANYLNAPHTHALEN-1-YL)SULFONYLAMINO]PENTANOIC HETNAM 2 8K0 ACID FORMUL 2 8K0 C15 H16 BR N O4 S FORMUL 3 HOH *90(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 ASN A 39 O GLU A 54 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 GLU A 129 N LYS A 9 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 107 O VAL A 114 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 PHE A 70 O SER A 82 SITE 1 AC1 13 MET A 20 THR A 74 ASP A 76 ARG A 78 SITE 2 AC1 13 GLN A 95 ILE A 104 ARG A 126 TYR A 128 SITE 3 AC1 13 HOH A 303 HOH A 313 HOH A 331 HOH A 333 SITE 4 AC1 13 HOH A 381 CRYST1 32.690 53.640 75.360 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 0.030590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013270 0.00000