HEADER TRANSFERASE 23-SEP-19 6KZD TITLE CRYSTAL STRUCTURE OF TRKC IN COMPLEX WITH 3-((6-(4-AMINOPHENYL) TITLE 2 IMIDAZO[1,2-A]PYRAZIN-3-YL)ETHYNYL)- N-(3-ISOPROPYL-5-((4- TITLE 3 METHYLPIPERAZIN-1-YL)METHYL)PHENYL)-2- METHYLBENZAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NT-3 GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GP145-TRKC,TRK-C,NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE COMPND 5 3,TRKC TYROSINE KINASE; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: SF FILE CONTAINS FRIEDEL PAIRS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NTRK3, TRKC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRKC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.WANG,Z.M.ZHANG REVDAT 2 27-MAR-24 6KZD 1 REMARK REVDAT 1 09-OCT-19 6KZD 0 JRNL AUTH S.CUI,Y.WANG,Y.WANG,X.TANG,X.REN,L.ZHANG,Y.XU,Z.ZHANG, JRNL AUTH 2 Z.M.ZHANG,X.LU,K.DING JRNL TITL DESIGN, SYNTHESIS AND BIOLOGICAL EVALUATION OF JRNL TITL 2 3-(IMIDAZO[1,2-A]PYRAZIN-3-YLETHYNYL)-2-METHYLBENZAMIDES AS JRNL TITL 3 POTENT AND SELECTIVE PAN-TROPOMYOSIN RECEPTOR KINASE (TRK) JRNL TITL 4 INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 179 470 2019 JRNL REFN ISSN 0223-5234 JRNL PMID 31271959 JRNL DOI 10.1016/J.EJMECH.2019.06.064 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 33905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.950 REMARK 3 FREE R VALUE TEST SET COUNT : 3087 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 0.0000 - 4.7821 0.99 2713 193 0.1841 0.1804 REMARK 3 2 4.7821 - 3.7968 1.00 2761 162 0.1409 0.1453 REMARK 3 3 3.7968 - 3.3171 1.00 2773 173 0.1444 0.1743 REMARK 3 4 3.3171 - 3.0140 0.98 2690 170 0.0000 0.2041 REMARK 3 5 3.0140 - 2.7980 0.99 2759 168 0.0000 0.1692 REMARK 3 6 2.7980 - 2.6331 1.00 2762 184 0.0000 0.1854 REMARK 3 7 2.6331 - 2.5012 1.00 2746 151 0.0000 0.1909 REMARK 3 8 2.5012 - 2.3924 1.00 2767 190 0.0000 0.1811 REMARK 3 9 2.3924 - 2.3003 1.00 2782 169 0.0000 0.1778 REMARK 3 10 2.3003 - 2.2209 0.99 2716 173 0.1450 0.1705 REMARK 3 11 2.2209 - 2.1515 0.96 2648 168 0.0000 0.2021 REMARK 3 12 2.1515 - 2.0900 0.83 2280 140 0.0000 0.2009 REMARK 3 13 2.0900 - 2.0350 0.80 2204 145 0.0000 0.1623 REMARK 3 14 2.0350 - 1.9853 0.73 2016 129 0.0000 0.1764 REMARK 3 15 1.9853 - 1.9402 0.66 1830 126 0.0000 0.2244 REMARK 3 16 1.9402 - 1.8989 0.61 1689 89 0.0000 0.2033 REMARK 3 17 1.8989 - 1.8609 0.57 1558 107 0.0000 0.2063 REMARK 3 18 1.8609 - 1.8258 0.54 1475 95 0.0000 0.2245 REMARK 3 19 1.8258 - 1.7932 0.53 1460 87 0.0000 0.2101 REMARK 3 20 1.7932 - 1.7628 0.52 1452 87 0.0000 0.2718 REMARK 3 21 1.7628 - 1.7344 0.51 1393 100 0.0000 0.2333 REMARK 3 22 1.7344 - 1.7080 0.49 1357 81 0.0000 0.2459 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.76 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 : 0.007 2361 REMARK 3 ANGLE : 1.103 3196 REMARK 3 CHIRALITY : 0.042 343 REMARK 3 PLANARITY : 0.006 400 REMARK 3 DIHEDRAL : 15.924 882 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 528 THROUGH 557 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4697 -27.2823 11.6747 REMARK 3 T TENSOR REMARK 3 T11: 0.1104 T22: 0.0887 REMARK 3 T33: 0.1584 T12: -0.0020 REMARK 3 T13: -0.0708 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0107 L22: 0.0350 REMARK 3 L33: 0.0043 L12: 0.0168 REMARK 3 L13: -0.0012 L23: -0.0048 REMARK 3 S TENSOR REMARK 3 S11: -0.0670 S12: 0.0227 S13: 0.0012 REMARK 3 S21: 0.0638 S22: 0.0417 S23: -0.1607 REMARK 3 S31: -0.0054 S32: -0.0462 S33: 0.0146 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 558 THROUGH 578 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3563 -27.7705 7.8327 REMARK 3 T TENSOR REMARK 3 T11: 0.0775 T22: 0.1322 REMARK 3 T33: 0.0990 T12: -0.0597 REMARK 3 T13: 0.0648 T23: -0.0392 REMARK 3 L TENSOR REMARK 3 L11: 0.0986 L22: 0.1868 REMARK 3 L33: 0.1261 L12: -0.1022 REMARK 3 L13: 0.0776 L23: -0.0085 REMARK 3 S TENSOR REMARK 3 S11: -0.1039 S12: 0.0651 S13: -0.0885 REMARK 3 S21: 0.0141 S22: 0.1847 S23: -0.1084 REMARK 3 S31: -0.0572 S32: 0.0096 S33: 0.0595 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 579 THROUGH 594 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.8269 -18.7180 13.2698 REMARK 3 T TENSOR REMARK 3 T11: 0.1526 T22: 0.1338 REMARK 3 T33: 0.1220 T12: -0.0144 REMARK 3 T13: 0.0325 T23: 0.0202 REMARK 3 L TENSOR REMARK 3 L11: 0.0261 L22: 0.0020 REMARK 3 L33: 0.0225 L12: 0.0072 REMARK 3 L13: 0.0206 L23: -0.0024 REMARK 3 S TENSOR REMARK 3 S11: -0.1796 S12: 0.0142 S13: -0.0386 REMARK 3 S21: 0.0196 S22: 0.0167 S23: 0.1229 REMARK 3 S31: -0.0354 S32: 0.0123 S33: -0.0069 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 595 THROUGH 652 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2739 -14.4396 11.9534 REMARK 3 T TENSOR REMARK 3 T11: 0.0564 T22: 0.0497 REMARK 3 T33: 0.0798 T12: -0.0076 REMARK 3 T13: -0.0045 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.0731 L22: 0.0697 REMARK 3 L33: 0.0772 L12: 0.0404 REMARK 3 L13: -0.0311 L23: -0.0269 REMARK 3 S TENSOR REMARK 3 S11: -0.0737 S12: -0.0073 S13: -0.0890 REMARK 3 S21: 0.0400 S22: 0.0739 S23: -0.1644 REMARK 3 S31: 0.1194 S32: 0.0144 S33: -0.0020 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 653 THROUGH 731 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2702 -5.8554 15.4473 REMARK 3 T TENSOR REMARK 3 T11: 0.0488 T22: 0.0740 REMARK 3 T33: 0.0424 T12: -0.0037 REMARK 3 T13: 0.0104 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.0458 L22: 0.1422 REMARK 3 L33: 0.0779 L12: -0.0071 REMARK 3 L13: 0.0229 L23: 0.0604 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: -0.0739 S13: 0.0323 REMARK 3 S21: -0.0051 S22: 0.0371 S23: -0.0263 REMARK 3 S31: 0.0044 S32: -0.0602 S33: -0.0007 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 732 THROUGH 816 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.4623 6.8867 21.6034 REMARK 3 T TENSOR REMARK 3 T11: 0.0378 T22: 0.0488 REMARK 3 T33: 0.0375 T12: 0.0164 REMARK 3 T13: 0.0207 T23: -0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.1667 L22: 0.0913 REMARK 3 L33: 0.1935 L12: -0.1002 REMARK 3 L13: 0.0323 L23: -0.0390 REMARK 3 S TENSOR REMARK 3 S11: -0.0654 S12: -0.1384 S13: 0.1784 REMARK 3 S21: 0.2072 S22: 0.0551 S23: -0.0476 REMARK 3 S31: -0.2043 S32: -0.0186 S33: -0.0382 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 817 THROUGH 837 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6278 3.9563 0.3633 REMARK 3 T TENSOR REMARK 3 T11: 0.1230 T22: 0.1166 REMARK 3 T33: 0.0843 T12: 0.0034 REMARK 3 T13: 0.0231 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.0434 L22: 0.0247 REMARK 3 L33: 0.0415 L12: 0.0305 REMARK 3 L13: 0.0312 L23: 0.0172 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: 0.1271 S13: -0.0660 REMARK 3 S21: -0.1283 S22: 0.0234 S23: -0.0290 REMARK 3 S31: 0.0255 S32: 0.0669 S33: 0.0004 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 6KZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300013909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33961 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.708 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1MMES, PH 6.0, 0.15M (NH4)2SO4, 15% REMARK 280 PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.84750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.42100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.28450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.42100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.84750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.28450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 637 REMARK 465 ILE A 638 REMARK 465 LEU A 639 REMARK 465 VAL A 640 REMARK 465 ASP A 641 REMARK 465 GLY A 642 REMARK 465 GLN A 643 REMARK 465 PRO A 644 REMARK 465 ARG A 645 REMARK 465 GLN A 646 REMARK 465 ALA A 647 REMARK 465 LYS A 648 REMARK 465 PHE A 713 REMARK 465 ASN A 714 REMARK 465 PRO A 715 REMARK 465 SER A 716 REMARK 465 GLY A 717 REMARK 465 ASN A 718 REMARK 465 ASP A 719 REMARK 465 PHE A 720 REMARK 465 CYS A 721 REMARK 465 ILE A 722 REMARK 465 TRP A 723 REMARK 465 CYS A 724 REMARK 465 GLU A 725 REMARK 465 VAL A 726 REMARK 465 GLY A 727 REMARK 465 GLY A 728 REMARK 465 LEU A 838 REMARK 465 GLY A 839 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 GLU A 546 CG CD OE1 OE2 REMARK 470 PHE A 549 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 575 CG CD CE NZ REMARK 470 ARG A 587 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 703 CG OD1 OD2 REMARK 470 LEU A 712 CG CD1 CD2 REMARK 470 HIS A 729 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 837 CG1 CG2 CD1 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 1108 O HOH A 1271 1.85 REMARK 500 O HOH A 1023 O HOH A 1069 1.86 REMARK 500 O HOH A 1251 O HOH A 1266 1.89 REMARK 500 O HOH A 1099 O HOH A 1248 1.90 REMARK 500 O4 PO4 A 902 O HOH A 1001 2.00 REMARK 500 O HOH A 1014 O HOH A 1250 2.01 REMARK 500 OE2 GLU A 790 O HOH A 1002 2.01 REMARK 500 O HOH A 1267 O HOH A 1276 2.05 REMARK 500 O HOH A 1071 O HOH A 1272 2.09 REMARK 500 N HIS A 729 O HOH A 1003 2.10 REMARK 500 O HOH A 1234 O HOH A 1267 2.10 REMARK 500 O HOH A 1134 O HOH A 1215 2.10 REMARK 500 OE2 GLU A 543 O HOH A 1004 2.11 REMARK 500 O HOH A 1020 O HOH A 1119 2.12 REMARK 500 O ARG A 787 O HOH A 1005 2.12 REMARK 500 O HOH A 1247 O HOH A 1265 2.14 REMARK 500 O HOH A 1297 O HOH A 1298 2.14 REMARK 500 O GLU A 650 O HOH A 1006 2.15 REMARK 500 OD2 ASP A 565 O HOH A 1007 2.16 REMARK 500 O HOH A 1062 O HOH A 1267 2.17 REMARK 500 O HOH A 1262 O HOH A 1276 2.17 REMARK 500 O HOH A 1250 O HOH A 1265 2.19 REMARK 500 O HOH A 1192 O HOH A 1236 2.19 REMARK 500 O HOH A 1247 O HOH A 1296 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1266 O HOH A 1274 4445 1.98 REMARK 500 O HOH A 1002 O HOH A 1102 3555 1.99 REMARK 500 O HOH A 1288 O HOH A 1295 1545 2.01 REMARK 500 O HOH A 1251 O HOH A 1274 4445 2.11 REMARK 500 O HOH A 1186 O HOH A 1275 4545 2.15 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 LYS A 564 -8.42 66.27 REMARK 500 ARG A 678 -8.79 77.13 REMARK 500 ASP A 679 45.76 -143.26 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 A1298 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1299 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A1300 DISTANCE = 7.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DZ6 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 902 DBREF 6KZD A 528 839 UNP Q16288 NTRK3_HUMAN 528 839 SEQRES 1 A 312 THR TYR VAL GLN HIS ILE LYS ARG ARG ASP ILE VAL LEU SEQRES 2 A 312 LYS ARG GLU LEU GLY GLU GLY ALA PHE GLY LYS VAL PHE SEQRES 3 A 312 LEU ALA GLU CYS TYR ASN LEU SER PRO THR LYS ASP LYS SEQRES 4 A 312 MET LEU VAL ALA VAL LYS ALA LEU LYS ASP PRO THR LEU SEQRES 5 A 312 ALA ALA ARG LYS ASP PHE GLN ARG GLU ALA GLU LEU LEU SEQRES 6 A 312 THR ASN LEU GLN HIS GLU HIS ILE VAL LYS PHE TYR GLY SEQRES 7 A 312 VAL CYS GLY ASP GLY ASP PRO LEU ILE MET VAL PHE GLU SEQRES 8 A 312 TYR MET LYS HIS GLY ASP LEU ASN LYS PHE LEU ARG ALA SEQRES 9 A 312 HIS GLY PRO ASP ALA MET ILE LEU VAL ASP GLY GLN PRO SEQRES 10 A 312 ARG GLN ALA LYS GLY GLU LEU GLY LEU SER GLN MET LEU SEQRES 11 A 312 HIS ILE ALA SER GLN ILE ALA SER GLY MET VAL TYR LEU SEQRES 12 A 312 ALA SER GLN HIS PHE VAL HIS ARG ASP LEU ALA THR ARG SEQRES 13 A 312 ASN CYS LEU VAL GLY ALA ASN LEU LEU VAL LYS ILE GLY SEQRES 14 A 312 ASP PHE GLY MET SER ARG ASP VAL TYR SER THR ASP TYR SEQRES 15 A 312 TYR ARG LEU PHE ASN PRO SER GLY ASN ASP PHE CYS ILE SEQRES 16 A 312 TRP CYS GLU VAL GLY GLY HIS THR MET LEU PRO ILE ARG SEQRES 17 A 312 TRP MET PRO PRO GLU SER ILE MET TYR ARG LYS PHE THR SEQRES 18 A 312 THR GLU SER ASP VAL TRP SER PHE GLY VAL ILE LEU TRP SEQRES 19 A 312 GLU ILE PHE THR TYR GLY LYS GLN PRO TRP PHE GLN LEU SEQRES 20 A 312 SER ASN THR GLU VAL ILE GLU CYS ILE THR GLN GLY ARG SEQRES 21 A 312 VAL LEU GLU ARG PRO ARG VAL CYS PRO LYS GLU VAL TYR SEQRES 22 A 312 ASP VAL MET LEU GLY CYS TRP GLN ARG GLU PRO GLN GLN SEQRES 23 A 312 ARG LEU ASN ILE LYS GLU ILE TYR LYS ILE LEU HIS ALA SEQRES 24 A 312 LEU GLY LYS ALA THR PRO ILE TYR LEU ASP ILE LEU GLY HET DZ6 A 901 44 HET PO4 A 902 5 HETNAM DZ6 3-[2-[6-(4-AMINOPHENYL)IMIDAZO[1,2-A]PYRAZIN-3- HETNAM 2 DZ6 YL]ETHYNYL]-2-METHYL-~{N}-[3-(4-METHYLPIPERAZIN-1-YL)- HETNAM 3 DZ6 5-PROPAN-2-YL-PHENYL]BENZAMIDE HETNAM PO4 PHOSPHATE ION FORMUL 2 DZ6 C36 H37 N7 O FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *300(H2 O) HELIX 1 AA1 LYS A 534 ARG A 536 5 3 HELIX 2 AA2 THR A 578 LEU A 595 1 18 HELIX 3 AA3 ASP A 624 HIS A 632 1 9 HELIX 4 AA4 GLY A 652 GLN A 673 1 22 HELIX 5 AA5 ALA A 681 ARG A 683 5 3 HELIX 6 AA6 ALA A 689 LEU A 691 5 3 HELIX 7 AA7 PRO A 733 MET A 737 5 5 HELIX 8 AA8 PRO A 738 ARG A 745 1 8 HELIX 9 AA9 THR A 748 THR A 765 1 18 HELIX 10 AB1 SER A 775 GLN A 785 1 11 HELIX 11 AB2 PRO A 796 TRP A 807 1 12 HELIX 12 AB3 GLU A 810 ARG A 814 5 5 HELIX 13 AB4 ASN A 816 GLY A 828 1 13 SHEET 1 AA1 5 ILE A 538 GLY A 547 0 SHEET 2 AA1 5 GLY A 550 CYS A 557 -1 O VAL A 552 N LEU A 544 SHEET 3 AA1 5 MET A 567 LEU A 574 -1 O ALA A 573 N LYS A 551 SHEET 4 AA1 5 LEU A 613 GLU A 618 -1 O PHE A 617 N ALA A 570 SHEET 5 AA1 5 PHE A 603 VAL A 606 -1 N GLY A 605 O VAL A 616 SHEET 1 AA2 2 CYS A 685 VAL A 687 0 SHEET 2 AA2 2 VAL A 693 ILE A 695 -1 O LYS A 694 N LEU A 686 SHEET 1 AA3 2 TYR A 710 ARG A 711 0 SHEET 2 AA3 2 MET A 731 LEU A 732 -1 O LEU A 732 N TYR A 710 CISPEP 1 ASP A 611 PRO A 612 0 4.59 SITE 1 AC1 18 ALA A 570 LYS A 572 GLU A 588 LEU A 591 SITE 2 AC1 18 LEU A 592 LEU A 595 VAL A 601 GLU A 618 SITE 3 AC1 18 TYR A 619 MET A 620 GLY A 623 HIS A 677 SITE 4 AC1 18 LEU A 686 GLY A 696 ASP A 697 PHE A 698 SITE 5 AC1 18 HOH A1012 HOH A1166 SITE 1 AC2 9 HIS A 532 ILE A 533 LYS A 534 ARG A 535 SITE 2 AC2 9 CYS A 607 GLY A 608 HOH A1001 HOH A1059 SITE 3 AC2 9 HOH A1064 CRYST1 51.695 54.569 108.842 90.00 90.00 90.00 P 21 21 21 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 0.019344 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009188 0.00000