HEADER PROTEIN BINDING 14-JAN-15 4XMB TITLE CRYSTAL STRUCTURE OF 2,2'-(NAPHTHALENE-1,4-DIYLBIS(((4-METHOXYPHENYL) TITLE 2 SULFONYL)AZANEDIYL))DIACETAMIDE BOUND TO HUMAN KEAP1 KELCH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KELCH DOMAIN (UNP RESIDUES 321-609); COMPND 5 SYNONYM: CYTOSOLIC INHIBITOR OF NRF2, INRF2, KELCH-LIKE PROTEIN 19, COMPND 6 KEAP1; 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 GENE: KEAP1, INRF2, KIAA0132, KLHL19; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NRF2 ACTIVATORS, CUL3, CULLIN3, BTB, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.P.LUCIANO,A.F.RYUZOJI,A.D.MESECAR REVDAT 2 27-SEP-23 4XMB 1 JRNL REMARK REVDAT 1 30-SEP-15 4XMB 0 JRNL AUTH A.D.JAIN,H.POTTETI,B.G.RICHARDSON,L.KINGSLEY,J.P.LUCIANO, JRNL AUTH 2 A.F.RYUZOJI,H.LEE,A.KRUNIC,A.D.MESECAR,S.P.REDDY,T.W.MOORE JRNL TITL PROBING THE STRUCTURAL REQUIREMENTS OF NON-ELECTROPHILIC JRNL TITL 2 NAPHTHALENE-BASED NRF2 ACTIVATORS. JRNL REF EUR.J.MED.CHEM. V. 103 252 2015 JRNL REFN ISSN 0223-5234 JRNL PMID 26363505 JRNL DOI 10.1016/J.EJMECH.2015.08.049 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 9401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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 27.7729 - 4.6375 0.97 1273 141 0.1643 0.2017 REMARK 3 2 4.6375 - 3.6837 0.93 1199 133 0.1387 0.1950 REMARK 3 3 3.6837 - 3.2188 0.95 1191 132 0.1515 0.1972 REMARK 3 4 3.2188 - 2.9249 0.95 1205 134 0.2048 0.2668 REMARK 3 5 2.9249 - 2.7154 0.96 1214 136 0.1973 0.2904 REMARK 3 6 2.7154 - 2.5554 0.96 1203 134 0.2091 0.2542 REMARK 3 7 2.5554 - 2.4275 0.92 1176 130 0.2004 0.3021 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.100 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 : 0.002 2303 REMARK 3 ANGLE : 0.656 3143 REMARK 3 CHIRALITY : 0.041 329 REMARK 3 PLANARITY : 0.002 414 REMARK 3 DIHEDRAL : 13.908 840 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 4XMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.547 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9899 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.428 REMARK 200 RESOLUTION RANGE LOW (A) : 32.971 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4IN4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM CHLORIDE, 20% W/V REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 25.76050 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ALA A 321 REMARK 465 PRO A 322 REMARK 465 LYS A 323 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 911 O HOH A 931 2.01 REMARK 500 O HOH A 902 O HOH A 905 2.07 REMARK 500 N GLY A 386 O HOH A 801 2.15 REMARK 500 NH1 ARG A 565 O HOH A 802 2.18 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 ARG A 336 -37.48 71.99 REMARK 500 VAL A 453 -168.00 -126.02 REMARK 500 GLN A 528 -34.66 -131.35 REMARK 500 VAL A 547 -166.11 -126.89 REMARK 500 SER A 592 138.09 177.20 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 932 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 943 DISTANCE = 6.57 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 41P A 701 DBREF 4XMB A 321 609 UNP Q14145 KEAP1_HUMAN 321 609 SEQRES 1 A 289 ALA PRO LYS VAL GLY ARG LEU ILE TYR THR ALA GLY GLY SEQRES 2 A 289 TYR PHE ARG GLN SER LEU SER TYR LEU GLU ALA TYR ASN SEQRES 3 A 289 PRO SER ASP GLY THR TRP LEU ARG LEU ALA ASP LEU GLN SEQRES 4 A 289 VAL PRO ARG SER GLY LEU ALA GLY CYS VAL VAL GLY GLY SEQRES 5 A 289 LEU LEU TYR ALA VAL GLY GLY ARG ASN ASN SER PRO ASP SEQRES 6 A 289 GLY ASN THR ASP SER SER ALA LEU ASP CYS TYR ASN PRO SEQRES 7 A 289 MET THR ASN GLN TRP SER PRO CYS ALA PRO MET SER VAL SEQRES 8 A 289 PRO ARG ASN ARG ILE GLY VAL GLY VAL ILE ASP GLY HIS SEQRES 9 A 289 ILE TYR ALA VAL GLY GLY SER HIS GLY CYS ILE HIS HIS SEQRES 10 A 289 ASN SER VAL GLU ARG TYR GLU PRO GLU ARG ASP GLU TRP SEQRES 11 A 289 HIS LEU VAL ALA PRO MET LEU THR ARG ARG ILE GLY VAL SEQRES 12 A 289 GLY VAL ALA VAL LEU ASN ARG LEU LEU TYR ALA VAL GLY SEQRES 13 A 289 GLY PHE ASP GLY THR ASN ARG LEU ASN SER ALA GLU CYS SEQRES 14 A 289 TYR TYR PRO GLU ARG ASN GLU TRP ARG MET ILE THR ALA SEQRES 15 A 289 MET ASN THR ILE ARG SER GLY ALA GLY VAL CYS VAL LEU SEQRES 16 A 289 HIS ASN CYS ILE TYR ALA ALA GLY GLY TYR ASP GLY GLN SEQRES 17 A 289 ASP GLN LEU ASN SER VAL GLU ARG TYR ASP VAL GLU THR SEQRES 18 A 289 GLU THR TRP THR PHE VAL ALA PRO MET LYS HIS ARG ARG SEQRES 19 A 289 SER ALA LEU GLY ILE THR VAL HIS GLN GLY ARG ILE TYR SEQRES 20 A 289 VAL LEU GLY GLY TYR ASP GLY HIS THR PHE LEU ASP SER SEQRES 21 A 289 VAL GLU CYS TYR ASP PRO ASP THR ASP THR TRP SER GLU SEQRES 22 A 289 VAL THR ARG MET THR SER GLY ARG SER GLY VAL GLY VAL SEQRES 23 A 289 ALA VAL THR HET 41P A 701 70 HETNAM 41P 2,2'-(NAPHTHALENE-1,4-DIYLBIS(((4-METHOXYPHENYL) HETNAM 2 41P SULFONYL)AZANEDIYL))DIACETAMIDE FORMUL 2 41P C28 H28 N4 O8 S2 FORMUL 3 HOH *143(H2 O) SHEET 1 AA1 4 THR A 351 ARG A 354 0 SHEET 2 AA1 4 LEU A 342 ASN A 346 -1 N ASN A 346 O THR A 351 SHEET 3 AA1 4 LEU A 327 ALA A 331 -1 N ILE A 328 O TYR A 345 SHEET 4 AA1 4 GLY A 605 THR A 609 -1 O ALA A 607 N TYR A 329 SHEET 1 AA2 4 ALA A 366 VAL A 370 0 SHEET 2 AA2 4 LEU A 373 VAL A 377 -1 O VAL A 377 N ALA A 366 SHEET 3 AA2 4 LEU A 393 TYR A 396 -1 O TYR A 396 N LEU A 374 SHEET 4 AA2 4 TRP A 403 PRO A 405 -1 O SER A 404 N CYS A 395 SHEET 1 AA3 4 GLY A 417 ILE A 421 0 SHEET 2 AA3 4 HIS A 424 VAL A 428 -1 O VAL A 428 N GLY A 417 SHEET 3 AA3 4 VAL A 440 TYR A 443 -1 O TYR A 443 N ILE A 425 SHEET 4 AA3 4 TRP A 450 LEU A 452 -1 O HIS A 451 N ARG A 442 SHEET 1 AA4 2 SER A 431 HIS A 432 0 SHEET 2 AA4 2 ILE A 435 HIS A 436 -1 O ILE A 435 N HIS A 432 SHEET 1 AA5 4 GLY A 464 VAL A 467 0 SHEET 2 AA5 4 LEU A 472 PHE A 478 -1 O VAL A 475 N GLY A 464 SHEET 3 AA5 4 ARG A 483 TYR A 490 -1 O TYR A 490 N LEU A 472 SHEET 4 AA5 4 TRP A 497 MET A 499 -1 O ARG A 498 N CYS A 489 SHEET 1 AA6 4 GLY A 511 LEU A 515 0 SHEET 2 AA6 4 CYS A 518 TYR A 525 -1 O ALA A 522 N GLY A 511 SHEET 3 AA6 4 GLN A 530 ASP A 538 -1 O GLU A 535 N ALA A 521 SHEET 4 AA6 4 THR A 543 PHE A 546 -1 O THR A 545 N ARG A 536 SHEET 1 AA7 4 GLY A 558 HIS A 562 0 SHEET 2 AA7 4 ARG A 565 LEU A 569 -1 O LEU A 569 N GLY A 558 SHEET 3 AA7 4 SER A 580 ASP A 585 -1 O TYR A 584 N ILE A 566 SHEET 4 AA7 4 THR A 590 ARG A 596 -1 O THR A 590 N ASP A 585 SITE 1 AC1 18 TYR A 334 SER A 363 GLY A 364 ARG A 380 SITE 2 AC1 18 ASN A 414 ARG A 415 ILE A 461 GLY A 462 SITE 3 AC1 18 PHE A 478 SER A 508 GLY A 509 TYR A 525 SITE 4 AC1 18 GLN A 530 SER A 555 ALA A 556 PHE A 577 SITE 5 AC1 18 SER A 602 GLY A 603 CRYST1 38.470 51.521 67.238 90.00 101.27 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 0.025994 0.000000 0.005179 0.00000 SCALE2 0.000000 0.019410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015165 0.00000