HEADER TRANSFERASE 11-JAN-19 6J5L TITLE CRYSTAL STRUCTURE OF TRK-A IN COMPLEX WITH THE PAN-TRK KINASE TITLE 2 INHIBITOR, COMPOUND 10E COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1,TRK1- COMPND 5 TRANSFORMING TYROSINE KINASE PROTEIN,TROPOMYOSIN-RELATED KINASE A, COMPND 6 TYROSINE KINASE RECEPTOR,TYROSINE KINASE RECEPTOR A,TRK-A,GP140TRK, COMPND 7 P140-TRKA; COMPND 8 EC: 2.7.10.1; COMPND 9 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: NTRK1, MTC, TRK, TRKA; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9 KEYWDS TRANSFERASE INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KENSUKE,I.KAZUTAKA REVDAT 4 22-NOV-23 6J5L 1 REMARK REVDAT 3 28-AUG-19 6J5L 1 JRNL REVDAT 2 24-JUL-19 6J5L 1 JRNL REVDAT 1 17-JUL-19 6J5L 0 JRNL AUTH H.SHIRAHASHI,E.TORIIHARA,Y.SUENAGA,H.YOSHIDA,K.AKAOGI, JRNL AUTH 2 Y.ENDOU,M.WAKABAYASHI,M.TAKASHIMA JRNL TITL THE DISCOVERY OF NOVEL 3-ARYL-INDAZOLE DERIVATIVES AS JRNL TITL 2 PERIPHERALLY RESTRICTED PAN-TRK INHIBITORS FOR THE TREATMENT JRNL TITL 3 OF PAIN. JRNL REF BIOORG.MED.CHEM.LETT. V. 29 2320 2019 JRNL REFN ESSN 1464-3405 JRNL PMID 31235262 JRNL DOI 10.1016/J.BMCL.2019.06.018 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 976 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1321 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3870 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2076 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.19000 REMARK 3 B22 (A**2) : 2.19000 REMARK 3 B33 (A**2) : -7.09000 REMARK 3 B12 (A**2) : 1.09000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.254 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.195 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2254 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1969 ; 0.004 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3075 ; 1.666 ; 1.705 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4512 ; 1.627 ; 1.644 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 5.539 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;30.533 ;21.196 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;17.674 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 284 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2566 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 513 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1129 ; 8.161 ; 7.750 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1128 ; 8.137 ; 7.748 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1406 ;11.054 ;11.611 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1407 ;11.052 ;11.615 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1125 ; 8.758 ; 7.830 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1126 ; 8.754 ; 7.829 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1670 ;11.969 ;11.536 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9051 ;15.677 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9045 ;15.681 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6J5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS OCT 15, 2015 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19224 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 44.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 1.43400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.6.04 REMARK 200 STARTING MODEL: 4AOJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.65 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CITRATE PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 52.09650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.07793 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 67.94600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 52.09650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.07793 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 67.94600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 52.09650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.07793 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 67.94600 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 52.09650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.07793 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 67.94600 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 52.09650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.07793 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 67.94600 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 52.09650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.07793 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 67.94600 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.15586 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 135.89200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 60.15586 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 135.89200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 60.15586 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 135.89200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 60.15586 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 135.89200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 60.15586 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 135.89200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 60.15586 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 135.89200 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: 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 GLY A 494 REMARK 465 ALA A 495 REMARK 465 MET A 496 REMARK 465 GLY A 497 REMARK 465 LEU A 533 REMARK 465 PRO A 534 REMARK 465 GLU A 535 REMARK 465 GLN A 536 REMARK 465 MET A 671 REMARK 465 SER A 672 REMARK 465 ARG A 673 REMARK 465 ASP A 674 REMARK 465 GLY A 684 REMARK 465 GLY A 685 REMARK 465 ARG A 686 REMARK 465 TYR A 791 REMARK 465 LEU A 792 REMARK 465 ASP A 793 REMARK 465 VAL A 794 REMARK 465 LEU A 795 REMARK 465 GLY A 796 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 ILE A 505 CD1 REMARK 470 LYS A 506 CG CD CE NZ REMARK 470 ARG A 507 NH1 NH2 REMARK 470 ARG A 508 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 509 CG OD1 OD2 REMARK 470 VAL A 511 CG1 CG2 REMARK 470 LYS A 513 NZ REMARK 470 GLU A 528 CG CD OE1 OE2 REMARK 470 HIS A 530 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 531 CG OD1 ND2 REMARK 470 LEU A 532 CG CD1 CD2 REMARK 470 ASP A 537 CG OD1 OD2 REMARK 470 LYS A 538 CG CD CE NZ REMARK 470 LEU A 546 CG CD1 CD2 REMARK 470 LYS A 547 CG CD CE NZ REMARK 470 GLU A 548 CG CD OE1 OE2 REMARK 470 SER A 550 OG REMARK 470 GLU A 551 CG CD OE1 OE2 REMARK 470 SER A 552 OG REMARK 470 ARG A 554 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 555 CG CD OE1 NE2 REMARK 470 ASP A 556 CG OD1 OD2 REMARK 470 ARG A 559 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 563 CD1 CD2 REMARK 470 LEU A 567 CD1 CD2 REMARK 470 GLN A 568 CG CD OE1 NE2 REMARK 470 GLN A 570 OE1 NE2 REMARK 470 ILE A 572 CD1 REMARK 470 ARG A 583 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 585 CG CD1 CD2 REMARK 470 ARG A 593 NE CZ NH1 NH2 REMARK 470 ARG A 602 NH1 NH2 REMARK 470 LYS A 609 CG CD CE NZ REMARK 470 LEU A 610 CD1 CD2 REMARK 470 LEU A 611 CD1 CD2 REMARK 470 ARG A 649 CD NE CZ NH1 NH2 REMARK 470 LEU A 651 CD1 CD2 REMARK 470 GLN A 660 OE1 NE2 REMARK 470 ILE A 675 CG1 CG2 CD1 REMARK 470 TYR A 676 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 677 OG REMARK 470 THR A 678 OG1 CG2 REMARK 470 ARG A 682 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 691 CD1 REMARK 470 LEU A 700 CD1 CD2 REMARK 470 LYS A 725 CG CD CE NZ REMARK 470 ARG A 744 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 747 CG CD OE1 OE2 REMARK 470 ARG A 750 NH1 NH2 REMARK 470 ILE A 759 CD1 REMARK 470 GLU A 767 CG CD OE1 OE2 REMARK 470 GLN A 769 CG CD OE1 NE2 REMARK 470 LYS A 775 CG CD CE NZ REMARK 470 ASP A 776 CG OD1 OD2 REMARK 470 GLN A 786 OE1 NE2 REMARK 470 VAL A 790 CG1 CG2 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 531 67.17 62.03 REMARK 500 GLU A 548 -130.36 54.86 REMARK 500 LYS A 609 -123.53 55.08 REMARK 500 ASP A 650 49.51 -140.04 REMARK 500 PHE A 669 -119.21 -117.90 REMARK 500 ALA A 787 56.94 -158.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B9C A 801 DBREF 6J5L A 502 796 UNP P04629 NTRK1_HUMAN 502 796 SEQADV 6J5L GLY A 494 UNP P04629 EXPRESSION TAG SEQADV 6J5L ALA A 495 UNP P04629 EXPRESSION TAG SEQADV 6J5L MET A 496 UNP P04629 EXPRESSION TAG SEQADV 6J5L GLY A 497 UNP P04629 EXPRESSION TAG SEQADV 6J5L SER A 498 UNP P04629 EXPRESSION TAG SEQADV 6J5L GLY A 499 UNP P04629 EXPRESSION TAG SEQADV 6J5L ILE A 500 UNP P04629 EXPRESSION TAG SEQADV 6J5L ARG A 501 UNP P04629 EXPRESSION TAG SEQRES 1 A 303 GLY ALA MET GLY SER GLY ILE ARG VAL HIS HIS ILE LYS SEQRES 2 A 303 ARG ARG ASP ILE VAL LEU LYS TRP GLU LEU GLY GLU GLY SEQRES 3 A 303 ALA PHE GLY LYS VAL PHE LEU ALA GLU CYS HIS ASN LEU SEQRES 4 A 303 LEU PRO GLU GLN ASP LYS MET LEU VAL ALA VAL LYS ALA SEQRES 5 A 303 LEU LYS GLU ALA SER GLU SER ALA ARG GLN ASP PHE GLN SEQRES 6 A 303 ARG GLU ALA GLU LEU LEU THR MET LEU GLN HIS GLN HIS SEQRES 7 A 303 ILE VAL ARG PHE PHE GLY VAL CYS THR GLU GLY ARG PRO SEQRES 8 A 303 LEU LEU MET VAL PHE GLU TYR MET ARG HIS GLY ASP LEU SEQRES 9 A 303 ASN ARG PHE LEU ARG SER HIS GLY PRO ASP ALA LYS LEU SEQRES 10 A 303 LEU ALA GLY GLY GLU ASP VAL ALA PRO GLY PRO LEU GLY SEQRES 11 A 303 LEU GLY GLN LEU LEU ALA VAL ALA SER GLN VAL ALA ALA SEQRES 12 A 303 GLY MET VAL TYR LEU ALA GLY LEU HIS PHE VAL HIS ARG SEQRES 13 A 303 ASP LEU ALA THR ARG ASN CYS LEU VAL GLY GLN GLY LEU SEQRES 14 A 303 VAL VAL LYS ILE GLY ASP PHE GLY MET SER ARG ASP ILE SEQRES 15 A 303 TYR SER THR ASP TYR TYR ARG VAL GLY GLY ARG THR MET SEQRES 16 A 303 LEU PRO ILE ARG TRP MET PRO PRO GLU SER ILE LEU TYR SEQRES 17 A 303 ARG LYS PHE THR THR GLU SER ASP VAL TRP SER PHE GLY SEQRES 18 A 303 VAL VAL LEU TRP GLU ILE PHE THR TYR GLY LYS GLN PRO SEQRES 19 A 303 TRP TYR GLN LEU SER ASN THR GLU ALA ILE ASP CYS ILE SEQRES 20 A 303 THR GLN GLY ARG GLU LEU GLU ARG PRO ARG ALA CYS PRO SEQRES 21 A 303 PRO GLU VAL TYR ALA ILE MET ARG GLY CYS TRP GLN ARG SEQRES 22 A 303 GLU PRO GLN GLN ARG HIS SER ILE LYS ASP VAL HIS ALA SEQRES 23 A 303 ARG LEU GLN ALA LEU ALA GLN ALA PRO PRO VAL TYR LEU SEQRES 24 A 303 ASP VAL LEU GLY HET B9C A 801 102 HETNAM B9C N-{2-[({3-[6-(PIPERAZIN-1-YL)PYRIDIN-3-YL]-1H-INDAZOL- HETNAM 2 B9C 5-YL}AMINO)METHYL]PHENYL}METHANESULFONAMIDE FORMUL 2 B9C C24 H27 N7 O2 S FORMUL 3 HOH *32(H2 O) HELIX 1 AA1 LYS A 506 ARG A 508 5 3 HELIX 2 AA2 SER A 552 LEU A 567 1 16 HELIX 3 AA3 LEU A 597 HIS A 604 1 8 HELIX 4 AA4 GLY A 605 LYS A 609 5 5 HELIX 5 AA5 GLY A 623 LEU A 644 1 22 HELIX 6 AA6 ALA A 652 ARG A 654 5 3 HELIX 7 AA7 PRO A 690 MET A 694 5 5 HELIX 8 AA8 PRO A 695 LEU A 700 1 6 HELIX 9 AA9 THR A 705 THR A 722 1 18 HELIX 10 AB1 SER A 732 GLY A 743 1 12 HELIX 11 AB2 PRO A 753 TRP A 764 1 12 HELIX 12 AB3 GLU A 767 ARG A 771 5 5 HELIX 13 AB4 SER A 773 GLN A 786 1 14 SHEET 1 AA1 5 ILE A 510 GLY A 519 0 SHEET 2 AA1 5 GLY A 522 CYS A 529 -1 O GLY A 522 N GLY A 519 SHEET 3 AA1 5 LEU A 540 LEU A 546 -1 O VAL A 541 N ALA A 527 SHEET 4 AA1 5 LEU A 586 GLU A 590 -1 O PHE A 589 N ALA A 542 SHEET 5 AA1 5 PHE A 575 CYS A 579 -1 N PHE A 576 O VAL A 588 SHEET 1 AA2 3 GLY A 595 ASP A 596 0 SHEET 2 AA2 3 CYS A 656 VAL A 658 -1 O VAL A 658 N GLY A 595 SHEET 3 AA2 3 VAL A 664 ILE A 666 -1 O LYS A 665 N LEU A 657 CISPEP 1 ARG A 583 PRO A 584 0 19.97 SITE 1 AC1 19 LEU A 516 GLY A 517 GLU A 518 PHE A 521 SITE 2 AC1 19 VAL A 524 ALA A 542 PHE A 589 GLU A 590 SITE 3 AC1 19 TYR A 591 MET A 592 GLY A 595 ASP A 596 SITE 4 AC1 19 LEU A 610 ALA A 612 ARG A 654 LEU A 657 SITE 5 AC1 19 ASP A 668 HOH A 902 HOH A 909 CRYST1 104.193 104.193 203.838 90.00 90.00 120.00 H 3 2 18 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 0.009598 0.005541 0.000000 0.00000 SCALE2 0.000000 0.011082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004906 0.00000