HEADER PROTEIN BINDING 24-APR-22 7XM2 TITLE CRYSTAL STRUCTURE OF KEAP1 KELCH DOMAIN (RESIDUES 322-609) IN COMPLEX TITLE 2 WITH NXPZ-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: CYTOSOLIC INHIBITOR OF NRF2,INRF2,KELCH-LIKE PROTEIN 19; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDATIVE STRESS SENSOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.XU REVDAT 2 29-NOV-23 7XM2 1 REMARK REVDAT 1 06-JUL-22 7XM2 0 JRNL AUTH G.LIU,R.HOU,L.XU,X.ZHANG,J.YAN,C.XING,K.XU,C.ZHUANG JRNL TITL CRYSTALLOGRAPHY-GUIDED OPTIMIZATIONS OF THE KEAP1-NRF2 JRNL TITL 2 INHIBITORS ON THE SOLVENT EXPOSED REGION: FROM SYMMETRIC TO JRNL TITL 3 ASYMMETRIC NAPHTHALENESULFONAMIDES. JRNL REF J.MED.CHEM. V. 65 8289 2022 JRNL REFN ISSN 0022-2623 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00170 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 19556 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) : 0.168 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3814 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 46.6700 - 6.8900 0.97 1246 137 0.1972 0.2396 REMARK 3 2 6.8900 - 5.4700 1.00 1277 142 0.1838 0.2454 REMARK 3 3 5.4700 - 4.7800 0.99 1285 142 0.1512 0.1604 REMARK 3 4 4.7800 - 4.3400 0.99 1262 141 0.1226 0.1468 REMARK 3 5 4.3400 - 4.0300 0.99 1267 143 0.1228 0.1688 REMARK 3 6 4.0300 - 3.7900 1.00 1288 146 0.1505 0.2097 REMARK 3 7 3.7900 - 3.6000 0.98 1244 139 0.1494 0.2183 REMARK 3 8 3.6000 - 3.4500 1.00 1282 144 0.1605 0.1785 REMARK 3 9 3.4500 - 3.3200 1.00 1274 145 0.1409 0.2079 REMARK 3 10 3.3100 - 3.2000 1.00 1276 145 0.1641 0.1880 REMARK 3 11 3.2000 - 3.1000 1.00 1291 138 0.1598 0.2215 REMARK 3 12 3.1000 - 3.0100 0.99 1258 143 0.1779 0.2373 REMARK 3 13 3.0100 - 2.9300 1.00 1281 139 0.1693 0.2238 REMARK 3 14 2.9300 - 2.8600 1.00 1276 143 0.1713 0.2361 REMARK 3 15 2.8600 - 2.8000 0.99 1269 140 0.1631 0.2022 REMARK 3 16 2.8000 - 2.7400 0.98 1251 139 0.1761 0.2562 REMARK 3 17 2.7400 - 2.6800 0.99 1278 142 0.2004 0.2720 REMARK 3 18 2.6800 - 2.6300 1.00 1279 143 0.1909 0.3168 REMARK 3 19 2.6300 - 2.5800 1.00 1274 140 0.2142 0.2807 REMARK 3 20 2.5800 - 2.5400 0.99 1252 142 0.2123 0.2516 REMARK 3 21 2.5400 - 2.5000 1.00 1302 142 0.2117 0.2884 REMARK 3 22 2.5000 - 2.4600 0.99 1291 140 0.2129 0.2931 REMARK 3 23 2.4600 - 2.4200 0.99 1228 139 0.2158 0.2584 REMARK 3 24 2.4200 - 2.3900 0.99 1345 147 0.2198 0.2411 REMARK 3 25 2.3900 - 2.3600 0.99 1231 139 0.2113 0.2144 REMARK 3 26 2.3600 - 2.3300 0.99 1251 137 0.2238 0.2663 REMARK 3 27 2.3300 - 2.3000 0.97 1223 137 0.2407 0.3096 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) : 0.261 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.773 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.07 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 2310 REMARK 3 ANGLE : 0.988 3157 REMARK 3 CHIRALITY : 0.056 324 REMARK 3 PLANARITY : 0.005 413 REMARK 3 DIHEDRAL : 16.847 338 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 7XM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL 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) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67000 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: 4XMB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M ZINC ACETATE DIHYDRATE, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.12800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.80950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.12800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.80950 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: X 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 GLY X 318 REMARK 465 SER X 319 REMARK 465 HIS X 320 REMARK 465 ALA X 321 REMARK 465 PRO X 322 REMARK 465 LYS X 323 REMARK 465 VAL X 324 REMARK 465 SER X 383 REMARK 465 PRO X 384 REMARK 465 ASP X 385 REMARK 465 GLY X 386 REMARK 465 ASN X 387 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 X 336 -18.76 71.83 REMARK 500 HIS X 575 -42.54 -135.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XM2 X 321 609 UNP Q14145 KEAP1_HUMAN 321 609 SEQADV 7XM2 GLY X 318 UNP Q14145 EXPRESSION TAG SEQADV 7XM2 SER X 319 UNP Q14145 EXPRESSION TAG SEQADV 7XM2 HIS X 320 UNP Q14145 EXPRESSION TAG SEQRES 1 X 292 GLY SER HIS ALA PRO LYS VAL GLY ARG LEU ILE TYR THR SEQRES 2 X 292 ALA GLY GLY TYR PHE ARG GLN SER LEU SER TYR LEU GLU SEQRES 3 X 292 ALA TYR ASN PRO SER ASP GLY THR TRP LEU ARG LEU ALA SEQRES 4 X 292 ASP LEU GLN VAL PRO ARG SER GLY LEU ALA GLY CYS VAL SEQRES 5 X 292 VAL GLY GLY LEU LEU TYR ALA VAL GLY GLY ARG ASN ASN SEQRES 6 X 292 SER PRO ASP GLY ASN THR ASP SER SER ALA LEU ASP CYS SEQRES 7 X 292 TYR ASN PRO MET THR ASN GLN TRP SER PRO CYS ALA PRO SEQRES 8 X 292 MET SER VAL PRO ARG ASN ARG ILE GLY VAL GLY VAL ILE SEQRES 9 X 292 ASP GLY HIS ILE TYR ALA VAL GLY GLY SER HIS GLY CYS SEQRES 10 X 292 ILE HIS HIS ASN SER VAL GLU ARG TYR GLU PRO GLU ARG SEQRES 11 X 292 ASP GLU TRP HIS LEU VAL ALA PRO MET LEU THR ARG ARG SEQRES 12 X 292 ILE GLY VAL GLY VAL ALA VAL LEU ASN ARG LEU LEU TYR SEQRES 13 X 292 ALA VAL GLY GLY PHE ASP GLY THR ASN ARG LEU ASN SER SEQRES 14 X 292 ALA GLU CYS TYR TYR PRO GLU ARG ASN GLU TRP ARG MET SEQRES 15 X 292 ILE THR ALA MET ASN THR ILE ARG SER GLY ALA GLY VAL SEQRES 16 X 292 CYS VAL LEU HIS ASN CYS ILE TYR ALA ALA GLY GLY TYR SEQRES 17 X 292 ASP GLY GLN ASP GLN LEU ASN SER VAL GLU ARG TYR ASP SEQRES 18 X 292 VAL GLU THR GLU THR TRP THR PHE VAL ALA PRO MET LYS SEQRES 19 X 292 HIS ARG ARG SER ALA LEU GLY ILE THR VAL HIS GLN GLY SEQRES 20 X 292 ARG ILE TYR VAL LEU GLY GLY TYR ASP GLY HIS THR PHE SEQRES 21 X 292 LEU ASP SER VAL GLU CYS TYR ASP PRO ASP THR ASP THR SEQRES 22 X 292 TRP SER GLU VAL THR ARG MET THR SER GLY ARG SER GLY SEQRES 23 X 292 VAL GLY VAL ALA VAL THR HET GFD X 701 68 HET GFD X 702 68 HETNAM GFD 2-[(4-AMINOPHENYL)SULFONYL-[4-[(2-AZANYL-2- HETNAM 2 GFD OXIDANYLIDENE-ETHYL)-(4-METHOXYPHENYL)SULFONYL- HETNAM 3 GFD AMINO]NAPHTHALEN-1-YL]AMINO]ETHANAMIDE FORMUL 2 GFD 2(C27 H27 N5 O7 S2) FORMUL 4 HOH *127(H2 O) SHEET 1 AA1 4 TRP X 352 ARG X 354 0 SHEET 2 AA1 4 LEU X 342 TYR X 345 -1 N ALA X 344 O LEU X 353 SHEET 3 AA1 4 LEU X 327 ALA X 331 -1 N THR X 330 O GLU X 343 SHEET 4 AA1 4 GLY X 605 THR X 609 -1 O GLY X 605 N ALA X 331 SHEET 1 AA2 4 ALA X 366 VAL X 370 0 SHEET 2 AA2 4 LEU X 373 VAL X 377 -1 O TYR X 375 N CYS X 368 SHEET 3 AA2 4 LEU X 393 TYR X 396 -1 O TYR X 396 N LEU X 374 SHEET 4 AA2 4 TRP X 403 PRO X 405 -1 O SER X 404 N CYS X 395 SHEET 1 AA3 4 GLY X 417 ILE X 421 0 SHEET 2 AA3 4 HIS X 424 VAL X 428 -1 O TYR X 426 N GLY X 419 SHEET 3 AA3 4 VAL X 440 GLU X 444 -1 O GLU X 441 N ALA X 427 SHEET 4 AA3 4 GLU X 449 VAL X 453 -1 O HIS X 451 N ARG X 442 SHEET 1 AA4 2 SER X 431 HIS X 432 0 SHEET 2 AA4 2 ILE X 435 HIS X 436 -1 O ILE X 435 N HIS X 432 SHEET 1 AA5 4 GLY X 464 LEU X 468 0 SHEET 2 AA5 4 LEU X 471 VAL X 475 -1 O TYR X 473 N ALA X 466 SHEET 3 AA5 4 ALA X 487 TYR X 491 -1 O TYR X 490 N LEU X 472 SHEET 4 AA5 4 GLU X 496 ILE X 500 -1 O ARG X 498 N CYS X 489 SHEET 1 AA6 4 GLY X 511 LEU X 515 0 SHEET 2 AA6 4 CYS X 518 ALA X 522 -1 O ALA X 522 N GLY X 511 SHEET 3 AA6 4 VAL X 534 ASP X 538 -1 O TYR X 537 N ILE X 519 SHEET 4 AA6 4 THR X 543 VAL X 547 -1 O VAL X 547 N VAL X 534 SHEET 1 AA7 4 GLY X 558 HIS X 562 0 SHEET 2 AA7 4 ARG X 565 LEU X 569 -1 O LEU X 569 N GLY X 558 SHEET 3 AA7 4 SER X 580 ASP X 585 -1 O TYR X 584 N ILE X 566 SHEET 4 AA7 4 THR X 590 ARG X 596 -1 O SER X 592 N CYS X 583 SSBOND 1 CYS X 434 CYS X 434 1555 2656 2.01 CRYST1 126.256 75.619 48.651 90.00 106.39 90.00 C 1 2 1 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 0.007920 0.000000 0.002329 0.00000 SCALE2 0.000000 0.013224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021425 0.00000