HEADER LYASE/LYAS INHIBITOR 08-AUG-18 6ECZ TITLE BIOREDUCTIVE 4-HYDROXY-3-NITRO-5-UREIDO-BENZENESULFONAMIDES TITLE 2 SELECTIVELY TARGET THE TUMOR-ASSOCIATED CARBONIC ANHYDRASE ISOFORMS TITLE 3 IX AND XII AND SHOW HYPOXIA-ENHANCED CYTOTOXICITY AGAINST HUMAN TITLE 4 CANCER CELL LINES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONIC ANHYDRASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBONATE DEHYDRATASE II,CARBONIC ANHYDRASE C,CAC,CARBONIC COMPND 5 ANHYDRASE II,CA-II; COMPND 6 EC: 4.2.1.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYPOXIA, CARBONIC ANHYDRASE IX, CARBONIC ANHYDRASE XII, INHIBITION, KEYWDS 2 ANTI-PROLIFERATIVE., LYASE, LYASE-LYAS INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SINGH,R.MCKENNA,C.T.SUPURAN,A.NOCENTINI,C.LOMELINO,E.LUCARINI, AUTHOR 2 G.BARTOLUCCI,L.D.C.MANNELLI,C.GHELARDINI,P.GRATTERI REVDAT 3 11-OCT-23 6ECZ 1 REMARK REVDAT 2 01-MAY-19 6ECZ 1 JRNL REVDAT 1 28-NOV-18 6ECZ 0 JRNL AUTH A.NOCENTINI,E.TRALLORI,S.SINGH,C.L.LOMELINO,G.BARTOLUCCI, JRNL AUTH 2 L.DI CESARE MANNELLI,C.GHELARDINI,R.MCKENNA,P.GRATTERI, JRNL AUTH 3 C.T.SUPURAN JRNL TITL 4-HYDROXY-3-NITRO-5-UREIDO-BENZENESULFONAMIDES SELECTIVELY JRNL TITL 2 TARGET THE TUMOR-ASSOCIATED CARBONIC ANHYDRASE ISOFORMS IX JRNL TITL 3 AND XII SHOWING HYPOXIA-ENHANCED ANTIPROLIFERATIVE PROFILES. JRNL REF J. MED. CHEM. V. 61 10860 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30433782 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01504 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10PRE_2097 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 12377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 618 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 29.4907 - 3.5035 0.99 3060 161 0.1309 0.1674 REMARK 3 2 3.5035 - 2.7815 0.97 2961 158 0.1818 0.2706 REMARK 3 3 2.7815 - 2.4301 0.96 2907 151 0.2087 0.2716 REMARK 3 4 2.4301 - 2.2080 0.95 2831 148 0.2066 0.2668 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.57 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 : 0.009 2140 REMARK 3 ANGLE : 1.408 2910 REMARK 3 CHIRALITY : 0.084 299 REMARK 3 PLANARITY : 0.012 376 REMARK 3 DIHEDRAL : 13.407 1713 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): -9.7255 -1.5831 16.0082 REMARK 3 T TENSOR REMARK 3 T11: 0.1699 T22: 0.1717 REMARK 3 T33: 0.1830 T12: -0.0071 REMARK 3 T13: 0.0005 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.8488 L22: 0.8922 REMARK 3 L33: 1.2080 L12: -0.2005 REMARK 3 L13: -0.0813 L23: -0.0675 REMARK 3 S TENSOR REMARK 3 S11: -0.0288 S12: -0.0168 S13: 0.0375 REMARK 3 S21: -0.0553 S22: 0.0107 S23: -0.0314 REMARK 3 S31: -0.0013 S32: 0.0261 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 6ECZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.8 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12387 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 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: PHENIX REMARK 200 STARTING MODEL: 3KS3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE, 50 MM TRIS-HCL, REMARK 280 PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.94200 REMARK 290 SMTRY3 2 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 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 65 -162.20 -161.58 REMARK 500 ASP A 71 109.97 -54.05 REMARK 500 ASP A 75 92.87 -64.16 REMARK 500 LYS A 127 -39.39 -31.02 REMARK 500 PHE A 176 71.03 -154.40 REMARK 500 ASN A 244 49.58 -93.50 REMARK 500 LYS A 252 -125.97 57.84 REMARK 500 ASN A 253 42.13 -95.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HIS A 96 NE2 111.6 REMARK 620 3 HIS A 119 ND1 114.7 93.1 REMARK 620 4 J4D A 302 N29 113.0 106.8 115.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J4D A 302 DBREF 6ECZ A 4 261 UNP P00918 CAH2_HUMAN 4 260 SEQRES 1 A 257 HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO GLU HIS TRP SEQRES 2 A 257 HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU ARG GLN SER SEQRES 3 A 257 PRO VAL ASP ILE ASP THR HIS THR ALA LYS TYR ASP PRO SEQRES 4 A 257 SER LEU LYS PRO LEU SER VAL SER TYR ASP GLN ALA THR SEQRES 5 A 257 SER LEU ARG ILE LEU ASN ASN GLY HIS ALA PHE ASN VAL SEQRES 6 A 257 GLU PHE ASP ASP SER GLN ASP LYS ALA VAL LEU LYS GLY SEQRES 7 A 257 GLY PRO LEU ASP GLY THR TYR ARG LEU ILE GLN PHE HIS SEQRES 8 A 257 PHE HIS TRP GLY SER LEU ASP GLY GLN GLY SER GLU HIS SEQRES 9 A 257 THR VAL ASP LYS LYS LYS TYR ALA ALA GLU LEU HIS LEU SEQRES 10 A 257 VAL HIS TRP ASN THR LYS TYR GLY ASP PHE GLY LYS ALA SEQRES 11 A 257 VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU GLY ILE PHE SEQRES 12 A 257 LEU LYS VAL GLY SER ALA LYS PRO GLY LEU GLN LYS VAL SEQRES 13 A 257 VAL ASP VAL LEU ASP SER ILE LYS THR LYS GLY LYS SER SEQRES 14 A 257 ALA ASP PHE THR ASN PHE ASP PRO ARG GLY LEU LEU PRO SEQRES 15 A 257 GLU SER LEU ASP TYR TRP THR TYR PRO GLY SER LEU THR SEQRES 16 A 257 THR PRO PRO LEU LEU GLU CYS VAL THR TRP ILE VAL LEU SEQRES 17 A 257 LYS GLU PRO ILE SER VAL SER SER GLU GLN VAL LEU LYS SEQRES 18 A 257 PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY GLU PRO GLU SEQRES 19 A 257 GLU LEU MET VAL ASP ASN TRP ARG PRO ALA GLN PRO LEU SEQRES 20 A 257 LYS ASN ARG GLN ILE LYS ALA SER PHE LYS HET ZN A 301 1 HET J4D A 302 29 HETNAM ZN ZINC ION HETNAM J4D 1-[3-NITRO-2-OXIDANYL-5-[OXIDANYL(OXIDANYLIDENE)- HETNAM 2 J4D $L^{4}-AZANYL]SULFONYL-PHENYL]-3-[2,3,4,5,6- HETNAM 3 J4D PENTAKIS(FLUORANYL)PHENYL]UREA FORMUL 2 ZN ZN 2+ FORMUL 3 J4D C13 H6 F5 N4 O8 S FORMUL 4 HOH *18(H2 O) HELIX 1 AA1 GLY A 12 ASP A 19 5 8 HELIX 2 AA2 PHE A 20 GLY A 25 5 6 HELIX 3 AA3 LYS A 127 GLY A 129 5 3 HELIX 4 AA4 ASP A 130 VAL A 135 1 6 HELIX 5 AA5 LYS A 154 GLY A 156 5 3 HELIX 6 AA6 LEU A 157 LEU A 164 1 8 HELIX 7 AA7 ASP A 165 LYS A 168 5 4 HELIX 8 AA8 ASP A 180 LEU A 185 5 6 HELIX 9 AA9 SER A 220 ARG A 227 1 8 SHEET 1 AA1 2 ASP A 32 ILE A 33 0 SHEET 2 AA1 2 THR A 108 VAL A 109 1 O THR A 108 N ILE A 33 SHEET 1 AA210 LYS A 39 TYR A 40 0 SHEET 2 AA210 LYS A 257 ALA A 258 1 O ALA A 258 N LYS A 39 SHEET 3 AA210 TYR A 191 GLY A 196 -1 N THR A 193 O LYS A 257 SHEET 4 AA210 VAL A 207 LEU A 212 -1 O VAL A 207 N GLY A 196 SHEET 5 AA210 LEU A 141 GLY A 151 1 N GLY A 145 O ILE A 210 SHEET 6 AA210 ALA A 116 ASN A 124 -1 N LEU A 118 O ILE A 146 SHEET 7 AA210 TYR A 88 TRP A 97 -1 N GLN A 92 O VAL A 121 SHEET 8 AA210 PHE A 66 PHE A 70 -1 N VAL A 68 O PHE A 93 SHEET 9 AA210 SER A 56 ASN A 61 -1 N LEU A 57 O GLU A 69 SHEET 10 AA210 SER A 173 ASP A 175 -1 O ALA A 174 N ILE A 59 SHEET 1 AA3 6 LEU A 47 SER A 50 0 SHEET 2 AA3 6 VAL A 78 GLY A 81 -1 O LYS A 80 N SER A 48 SHEET 3 AA3 6 TYR A 88 TRP A 97 -1 O TYR A 88 N LEU A 79 SHEET 4 AA3 6 ALA A 116 ASN A 124 -1 O VAL A 121 N GLN A 92 SHEET 5 AA3 6 LEU A 141 GLY A 151 -1 O ILE A 146 N LEU A 118 SHEET 6 AA3 6 ILE A 216 SER A 219 1 O VAL A 218 N GLY A 151 LINK NE2 HIS A 94 ZN ZN A 301 1555 1555 2.03 LINK NE2 HIS A 96 ZN ZN A 301 1555 1555 2.10 LINK ND1 HIS A 119 ZN ZN A 301 1555 1555 2.07 LINK ZN ZN A 301 N29 J4D A 302 1555 1555 1.92 CISPEP 1 SER A 29 PRO A 30 0 -0.28 CISPEP 2 PRO A 201 PRO A 202 0 4.82 SITE 1 AC1 4 HIS A 94 HIS A 96 HIS A 119 J4D A 302 SITE 1 AC2 10 ASN A 62 HIS A 64 ASN A 67 GLN A 92 SITE 2 AC2 10 HIS A 94 HIS A 96 HIS A 119 LEU A 198 SITE 3 AC2 10 THR A 199 ZN A 301 CRYST1 42.880 41.884 72.905 90.00 104.45 90.00 P 1 21 1 2 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 0.023321 0.000000 0.006010 0.00000 SCALE2 0.000000 0.023875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014165 0.00000