HEADER TRANSFERASE/INHIBITOR 02-DEC-21 7T1T TITLE JAK2 JH2 IN COMPLEX WITH JAK292 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE JAK2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JANUS KINASE 2,JAK-2; COMPND 5 EC: 2.7.10.2; 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: JAK2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PSEUDOKINASE DOMAIN, INHIBITOR, COMPLEX, TRANSFERASE, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.IPPOLITO,S.HENRY,S.G.KRIMMER,J.SCHLESSINGER,W.L.JORGENSEN REVDAT 2 18-OCT-23 7T1T 1 REMARK REVDAT 1 25-MAY-22 7T1T 0 JRNL AUTH S.P.HENRY,M.E.LIOSI,J.A.IPPOLITO,K.J.CUTRONA,S.G.KRIMMER, JRNL AUTH 2 A.S.NEWTON,J.SCHLESSINGER,W.L.JORGENSEN JRNL TITL CONVERSION OF A FALSE VIRTUAL SCREEN HIT INTO SELECTIVE JAK2 JRNL TITL 2 JH2 DOMAIN BINDERS USING CONVERGENT DESIGN STRATEGIES JRNL REF ACS MED.CHEM.LETT. V. 13 819 2022 JRNL REFN ISSN 1948-5875 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00051 REMARK 2 REMARK 2 RESOLUTION. 2.08 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 17068 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 849 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 23.6300 - 3.7800 0.99 2800 148 0.1603 0.1893 REMARK 3 2 3.7800 - 3.0000 0.99 2738 145 0.1756 0.2209 REMARK 3 3 3.0000 - 2.6200 0.99 2711 137 0.1977 0.2486 REMARK 3 4 2.6200 - 2.3800 0.98 2691 143 0.1923 0.2601 REMARK 3 5 2.3800 - 2.2100 0.97 2657 138 0.1993 0.2627 REMARK 3 6 2.2100 - 2.0800 0.95 2622 138 0.2124 0.2875 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) : 23.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.23 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 7T1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17077 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 23.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.617 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.31 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.650 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: 4FVP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, REMARK 280 0.001 M TCEP, 12-24% PEG 4,000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 28.80000 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 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 THR A 810 REMARK 465 PRO A 811 REMARK 465 ASP A 812 REMARK 465 LEU A 813 REMARK 465 VAL A 814 REMARK 465 PRO A 815 REMARK 465 ARG A 816 REMARK 465 GLY A 817 REMARK 465 SER A 818 REMARK 465 HIS A 819 REMARK 465 HIS A 820 REMARK 465 HIS A 821 REMARK 465 HIS A 822 REMARK 465 HIS A 823 REMARK 465 HIS A 824 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 558 CG CD CE NZ REMARK 470 ARG A 565 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 572 CG CD OE1 NE2 REMARK 470 LYS A 585 CG CD CE NZ REMARK 470 ARG A 588 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 639 CG CD CE NZ REMARK 470 LYS A 640 CG CD CE NZ REMARK 470 ASN A 643 CG OD1 ND2 REMARK 470 ARG A 687 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 688 CG CD CE NZ REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 LYS A 728 CG CD CE NZ REMARK 470 GLN A 760 CG CD OE1 NE2 REMARK 470 LYS A 776 CG CD CE NZ REMARK 470 ARG A 799 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 809 CG CD1 CD2 CE1 CE2 CZ 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 ASN A 548 -136.96 -113.90 REMARK 500 CYS A 644 26.60 -159.47 REMARK 500 ASN A 673 52.40 -148.30 REMARK 500 ASN A 673 49.96 -147.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 7T1T A 536 812 UNP O60674 JAK2_HUMAN 536 812 SEQADV 7T1T ALA A 659 UNP O60674 TRP 659 ENGINEERED MUTATION SEQADV 7T1T ALA A 777 UNP O60674 TRP 777 ENGINEERED MUTATION SEQADV 7T1T HIS A 794 UNP O60674 PHE 794 ENGINEERED MUTATION SEQADV 7T1T LEU A 813 UNP O60674 EXPRESSION TAG SEQADV 7T1T VAL A 814 UNP O60674 EXPRESSION TAG SEQADV 7T1T PRO A 815 UNP O60674 EXPRESSION TAG SEQADV 7T1T ARG A 816 UNP O60674 EXPRESSION TAG SEQADV 7T1T GLY A 817 UNP O60674 EXPRESSION TAG SEQADV 7T1T SER A 818 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 819 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 820 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 821 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 822 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 823 UNP O60674 EXPRESSION TAG SEQADV 7T1T HIS A 824 UNP O60674 EXPRESSION TAG SEQRES 1 A 289 VAL PHE HIS LYS ILE ARG ASN GLU ASP LEU ILE PHE ASN SEQRES 2 A 289 GLU SER LEU GLY GLN GLY THR PHE THR LYS ILE PHE LYS SEQRES 3 A 289 GLY VAL ARG ARG GLU VAL GLY ASP TYR GLY GLN LEU HIS SEQRES 4 A 289 GLU THR GLU VAL LEU LEU LYS VAL LEU ASP LYS ALA HIS SEQRES 5 A 289 ARG ASN TYR SER GLU SER PHE PHE GLU ALA ALA SER MET SEQRES 6 A 289 MET SER LYS LEU SER HIS LYS HIS LEU VAL LEU ASN TYR SEQRES 7 A 289 GLY VAL CYS VAL CYS GLY ASP GLU ASN ILE LEU VAL GLN SEQRES 8 A 289 GLU PHE VAL LYS PHE GLY SER LEU ASP THR TYR LEU LYS SEQRES 9 A 289 LYS ASN LYS ASN CYS ILE ASN ILE LEU TRP LYS LEU GLU SEQRES 10 A 289 VAL ALA LYS GLN LEU ALA ALA ALA MET HIS PHE LEU GLU SEQRES 11 A 289 GLU ASN THR LEU ILE HIS GLY ASN VAL CYS ALA LYS ASN SEQRES 12 A 289 ILE LEU LEU ILE ARG GLU GLU ASP ARG LYS THR GLY ASN SEQRES 13 A 289 PRO PRO PHE ILE LYS LEU SER ASP PRO GLY ILE SER ILE SEQRES 14 A 289 THR VAL LEU PRO LYS ASP ILE LEU GLN GLU ARG ILE PRO SEQRES 15 A 289 TRP VAL PRO PRO GLU CYS ILE GLU ASN PRO LYS ASN LEU SEQRES 16 A 289 ASN LEU ALA THR ASP LYS TRP SER PHE GLY THR THR LEU SEQRES 17 A 289 TRP GLU ILE CYS SER GLY GLY ASP LYS PRO LEU SER ALA SEQRES 18 A 289 LEU ASP SER GLN ARG LYS LEU GLN PHE TYR GLU ASP ARG SEQRES 19 A 289 HIS GLN LEU PRO ALA PRO LYS ALA ALA GLU LEU ALA ASN SEQRES 20 A 289 LEU ILE ASN ASN CYS MET ASP TYR GLU PRO ASP HIS ARG SEQRES 21 A 289 PRO SER PHE ARG ALA ILE ILE ARG ASP LEU ASN SER LEU SEQRES 22 A 289 PHE THR PRO ASP LEU VAL PRO ARG GLY SER HIS HIS HIS SEQRES 23 A 289 HIS HIS HIS HET E8I A 901 33 HET GOL A 902 6 HETNAM E8I (2S)-2-[({4-[(2-AMINO-7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL) HETNAM 2 E8I OXY]PHENYL}CARBAMOYL)AMINO]-4-PHENYLBUTANOIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 E8I C23 H22 N6 O4 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *129(H2 O) HELIX 1 AA1 ARG A 541 GLU A 543 5 3 HELIX 2 AA2 ASP A 569 GLY A 571 5 3 HELIX 3 AA3 LYS A 585 ASN A 589 5 5 HELIX 4 AA4 TYR A 590 LEU A 604 1 15 HELIX 5 AA5 SER A 633 ASN A 641 1 9 HELIX 6 AA6 LYS A 642 ILE A 645 5 4 HELIX 7 AA7 ASN A 646 ASN A 667 1 22 HELIX 8 AA8 CYS A 675 LYS A 677 5 3 HELIX 9 AA9 PRO A 708 ARG A 715 1 8 HELIX 10 AB1 PRO A 720 ASN A 726 1 7 HELIX 11 AB2 PRO A 727 LEU A 730 5 4 HELIX 12 AB3 ASN A 731 SER A 748 1 18 HELIX 13 AB4 ASP A 758 ASP A 768 1 11 HELIX 14 AB5 ALA A 777 GLU A 779 5 3 HELIX 15 AB6 LEU A 780 MET A 788 1 9 HELIX 16 AB7 GLU A 791 ARG A 795 5 5 HELIX 17 AB8 SER A 797 SER A 807 1 11 SHEET 1 AA1 5 LEU A 545 GLY A 554 0 SHEET 2 AA1 5 THR A 557 VAL A 567 -1 O ILE A 559 N LEU A 551 SHEET 3 AA1 5 LEU A 573 LEU A 583 -1 O HIS A 574 N GLU A 566 SHEET 4 AA1 5 ILE A 623 GLU A 627 -1 O GLN A 626 N LEU A 579 SHEET 5 AA1 5 ASN A 612 CYS A 616 -1 N GLY A 614 O VAL A 625 SHEET 1 AA2 2 ILE A 679 ARG A 683 0 SHEET 2 AA2 2 PHE A 694 LEU A 697 -1 O LYS A 696 N LEU A 680 CISPEP 1 ILE A 716 PRO A 717 0 6.77 CRYST1 44.530 57.600 60.980 90.00 110.81 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 0.022457 0.000000 0.008533 0.00000 SCALE2 0.000000 0.017361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017543 0.00000