HEADER LIPID BINDING PROTEIN 17-DEC-19 6LJT TITLE CRYSTAL STRUCTURE OF HUMAN FABP4 IN COMPLEX WITH A NOVEL INHIBITOR 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 FABP4, INHIBITOR, COMPLEX, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.X.SU,X.L.ZHANG,M.J.LI,Y.C.XU REVDAT 3 22-NOV-23 6LJT 1 REMARK REVDAT 2 06-MAY-20 6LJT 1 JRNL REVDAT 1 15-APR-20 6LJT 0 JRNL AUTH H.SU,Y.ZOU,G.CHEN,H.DOU,H.XIE,X.YUAN,X.ZHANG,N.ZHANG,M.LI, JRNL AUTH 2 Y.XU JRNL TITL EXPLORATION OF FRAGMENT BINDING POSES LEADING TO EFFICIENT JRNL TITL 2 DISCOVERY OF HIGHLY POTENT AND ORALLY EFFECTIVE INHIBITORS JRNL TITL 3 OF FABP4 FOR ANTI-INFLAMMATION. JRNL REF J.MED.CHEM. V. 63 4090 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32202425 JRNL DOI 10.1021/ACS.JMEDCHEM.9B02107 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1184 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 37.5100 - 2.8996 1.00 3012 159 0.1769 0.1802 REMARK 3 2 2.8996 - 2.3016 1.00 2886 147 0.1925 0.1926 REMARK 3 3 2.3016 - 2.0107 1.00 2855 138 0.1778 0.1929 REMARK 3 4 2.0107 - 1.8269 1.00 2818 166 0.1759 0.2175 REMARK 3 5 1.8269 - 1.6959 1.00 2797 150 0.1859 0.2166 REMARK 3 6 1.6959 - 1.5959 0.99 2814 133 0.1939 0.1975 REMARK 3 7 1.5959 - 1.5160 0.99 2788 146 0.1916 0.2184 REMARK 3 8 1.5160 - 1.4500 0.96 2674 145 0.2120 0.2363 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 : 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) : 19.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.61 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 1106 REMARK 3 ANGLE : 0.784 1485 REMARK 3 CHIRALITY : 0.076 168 REMARK 3 PLANARITY : 0.004 186 REMARK 3 DIHEDRAL : 8.842 663 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 7.5982 -9.8577 -14.7599 REMARK 3 T TENSOR REMARK 3 T11: 0.0741 T22: 0.0988 REMARK 3 T33: 0.1036 T12: -0.0034 REMARK 3 T13: -0.0120 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.0586 L22: 1.9647 REMARK 3 L33: 1.0532 L12: -0.2880 REMARK 3 L13: -0.3075 L23: -0.4156 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: 0.0058 S13: -0.0018 REMARK 3 S21: -0.0615 S22: 0.0366 S23: 0.0564 REMARK 3 S31: 0.0139 S32: -0.0093 S33: -0.0587 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 6LJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-18 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 4NNT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TRISODIUM CITRATE, PH 6.5, 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 16.17650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.50950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.98850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.50950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.17650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.98850 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 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 -134.87 53.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 395 DISTANCE = 6.35 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EH6 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 DBREF 6LJT A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 6LJT MET A -20 UNP P15090 EXPRESSION TAG SEQADV 6LJT GLY A -19 UNP P15090 EXPRESSION TAG SEQADV 6LJT SER A -18 UNP P15090 EXPRESSION TAG SEQADV 6LJT SER A -17 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -16 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -15 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -14 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -13 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -12 UNP P15090 EXPRESSION TAG SEQADV 6LJT HIS A -11 UNP P15090 EXPRESSION TAG SEQADV 6LJT SER A -10 UNP P15090 EXPRESSION TAG SEQADV 6LJT SER A -9 UNP P15090 EXPRESSION TAG SEQADV 6LJT GLY A -8 UNP P15090 EXPRESSION TAG SEQADV 6LJT LEU A -7 UNP P15090 EXPRESSION TAG SEQADV 6LJT VAL A -6 UNP P15090 EXPRESSION TAG SEQADV 6LJT PRO A -5 UNP P15090 EXPRESSION TAG SEQADV 6LJT ARG A -4 UNP P15090 EXPRESSION TAG SEQADV 6LJT GLY A -3 UNP P15090 EXPRESSION TAG SEQADV 6LJT SER A -2 UNP P15090 EXPRESSION TAG SEQADV 6LJT 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 EH6 A 201 23 HET EDO A 202 4 HETNAM EH6 2-[(3-CHLORANYL-2-PHENYL-PHENYL)AMINO]BENZOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EH6 C19 H14 CL N O2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *95(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 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 GLU A 72 O VAL A 80 SITE 1 AC1 9 PHE A 16 ALA A 33 PHE A 57 ALA A 75 SITE 2 AC1 9 ASP A 76 ARG A 106 ARG A 126 TYR A 128 SITE 3 AC1 9 HOH A 322 SITE 1 AC2 6 ILE A 51 THR A 60 ARG A 106 HOH A 319 SITE 2 AC2 6 HOH A 331 HOH A 354 CRYST1 32.353 53.977 75.019 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 0.030909 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013330 0.00000