HEADER ISOMERASE 06-APR-21 7EKV TITLE CRYSTAL STRUCTURE OF HUMAN PIN1 COMPLEXED WITH A COVALENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PIN1,PPIASE PIN1, COMPND 5 ROTAMASE PIN1; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COVALENT, INHIBITOR, COMPLEX, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,J.LI REVDAT 3 29-NOV-23 7EKV 1 REMARK REVDAT 2 23-FEB-22 7EKV 1 JRNL REVDAT 1 16-FEB-22 7EKV 0 JRNL AUTH L.LIU,R.ZHU,J.LI,Y.PEI,S.WANG,P.XU,M.WANG,Y.WEN,H.ZHANG, JRNL AUTH 2 D.DU,H.DING,H.JIANG,K.CHEN,B.ZHOU,L.YU,C.LUO JRNL TITL COMPUTATIONAL AND STRUCTURE-BASED DEVELOPMENT OF HIGH POTENT JRNL TITL 2 CELL-ACTIVE COVALENT INHIBITOR TARGETING THE PEPTIDYL-PROLYL JRNL TITL 3 ISOMERASE NIMA-INTERACTING-1 (PIN1). JRNL REF J.MED.CHEM. V. 65 2174 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35089030 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01686 REMARK 2 REMARK 2 RESOLUTION. 1.95 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1630 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 33.1300 - 4.4600 1.00 1323 145 0.1932 0.1891 REMARK 3 2 4.4600 - 3.5400 1.00 1255 135 0.1553 0.2059 REMARK 3 3 3.5400 - 3.0900 1.00 1226 142 0.1879 0.2374 REMARK 3 4 3.0900 - 2.8100 1.00 1237 133 0.1987 0.2355 REMARK 3 5 2.8100 - 2.6100 1.00 1210 139 0.2079 0.2663 REMARK 3 6 2.6100 - 2.4600 1.00 1210 128 0.2107 0.2608 REMARK 3 7 2.4500 - 2.3300 1.00 1232 134 0.2216 0.2839 REMARK 3 8 2.3300 - 2.2300 1.00 1199 134 0.2176 0.2530 REMARK 3 9 2.2300 - 2.1400 1.00 1216 138 0.2093 0.2354 REMARK 3 10 2.1400 - 2.0700 1.00 1201 135 0.2096 0.2565 REMARK 3 11 2.0700 - 2.0100 1.00 1215 134 0.2272 0.2495 REMARK 3 12 2.0100 - 1.9500 0.99 1172 133 0.2363 0.2907 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.11 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7EKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021643. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4-7.6 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : 0.08031 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: PHASER REMARK 200 STARTING MODEL: 3NTP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 1% PEG400, 100MM REMARK 280 HEPES, PH 7.5, PH 7.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.60433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.20867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.20867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.60433 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: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8640 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER 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 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 39 REMARK 465 ASN A 40 REMARK 465 SER A 41 REMARK 465 SER A 42 REMARK 465 SER A 43 REMARK 465 GLY A 44 REMARK 465 GLY A 45 REMARK 465 LYS A 46 REMARK 465 ASN A 47 REMARK 465 GLY A 48 REMARK 465 GLN A 49 REMARK 465 GLY A 50 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 LEU A 7 124.10 72.97 REMARK 500 ASP A 112 39.52 -84.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EKV A 1 163 UNP Q13526 PIN1_HUMAN 1 163 SEQADV 7EKV MET A -19 UNP Q13526 INITIATING METHIONINE SEQADV 7EKV GLY A -18 UNP Q13526 EXPRESSION TAG SEQADV 7EKV SER A -17 UNP Q13526 EXPRESSION TAG SEQADV 7EKV SER A -16 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -15 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -14 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -13 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -12 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -11 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A -10 UNP Q13526 EXPRESSION TAG SEQADV 7EKV SER A -9 UNP Q13526 EXPRESSION TAG SEQADV 7EKV SER A -8 UNP Q13526 EXPRESSION TAG SEQADV 7EKV GLY A -7 UNP Q13526 EXPRESSION TAG SEQADV 7EKV LEU A -6 UNP Q13526 EXPRESSION TAG SEQADV 7EKV VAL A -5 UNP Q13526 EXPRESSION TAG SEQADV 7EKV PRO A -4 UNP Q13526 EXPRESSION TAG SEQADV 7EKV ARG A -3 UNP Q13526 EXPRESSION TAG SEQADV 7EKV GLY A -2 UNP Q13526 EXPRESSION TAG SEQADV 7EKV SER A -1 UNP Q13526 EXPRESSION TAG SEQADV 7EKV HIS A 0 UNP Q13526 EXPRESSION TAG SEQADV 7EKV ALA A 14 UNP Q13526 ARG 14 ENGINEERED MUTATION SEQRES 1 A 183 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 183 LEU VAL PRO ARG GLY SER HIS MET ALA ASP GLU GLU LYS SEQRES 3 A 183 LEU PRO PRO GLY TRP GLU LYS ALA MET SER ARG SER SER SEQRES 4 A 183 GLY ARG VAL TYR TYR PHE ASN HIS ILE THR ASN ALA SER SEQRES 5 A 183 GLN TRP GLU ARG PRO SER GLY ASN SER SER SER GLY GLY SEQRES 6 A 183 LYS ASN GLY GLN GLY GLU PRO ALA ARG VAL ARG CYS SER SEQRES 7 A 183 HIS LEU LEU VAL LYS HIS SER GLN SER ARG ARG PRO SER SEQRES 8 A 183 SER TRP ARG GLN GLU LYS ILE THR ARG THR LYS GLU GLU SEQRES 9 A 183 ALA LEU GLU LEU ILE ASN GLY TYR ILE GLN LYS ILE LYS SEQRES 10 A 183 SER GLY GLU GLU ASP PHE GLU SER LEU ALA SER GLN PHE SEQRES 11 A 183 SER ASP CYS SER SER ALA LYS ALA ARG GLY ASP LEU GLY SEQRES 12 A 183 ALA PHE SER ARG GLY GLN MET GLN LYS PRO PHE GLU ASP SEQRES 13 A 183 ALA SER PHE ALA LEU ARG THR GLY GLU MET SER GLY PRO SEQRES 14 A 183 VAL PHE THR ASP SER GLY ILE HIS ILE ILE LEU ARG THR SEQRES 15 A 183 GLU HET J50 A 201 26 HET PE8 A 202 25 HETNAM J50 8-(2-CHLOROACETYL)-4-((5-PHENYLFURAN-2-YL)METHYL)-1- HETNAM 2 J50 THIA-4,8-DIAZASPIRO[4.5]DECAN-3-ONE HETNAM PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL FORMUL 2 J50 C20 H21 CL N2 O3 S FORMUL 3 PE8 C16 H34 O9 FORMUL 4 HOH *171(H2 O) HELIX 1 AA1 THR A 81 SER A 98 1 18 HELIX 2 AA2 ASP A 102 SER A 111 1 10 HELIX 3 AA3 CYS A 113 ARG A 119 5 7 HELIX 4 AA4 GLN A 131 LEU A 141 1 11 SHEET 1 AA1 3 TRP A 11 MET A 15 0 SHEET 2 AA1 3 VAL A 22 ASN A 26 -1 O PHE A 25 N GLU A 12 SHEET 3 AA1 3 SER A 32 GLN A 33 -1 O GLN A 33 N TYR A 24 SHEET 1 AA2 4 ASP A 121 SER A 126 0 SHEET 2 AA2 4 ARG A 54 VAL A 62 -1 N CYS A 57 O LEU A 122 SHEET 3 AA2 4 GLY A 155 GLU A 163 -1 O LEU A 160 N SER A 58 SHEET 4 AA2 4 VAL A 150 THR A 152 -1 N VAL A 150 O HIS A 157 LINK SG CYS A 113 C24 J50 A 201 1555 1555 1.70 CRYST1 68.637 68.637 79.813 90.00 90.00 120.00 P 31 2 1 6 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 0.014569 0.008412 0.000000 0.00000 SCALE2 0.000000 0.016823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012529 0.00000