PDB Short entry for 3EFJ HEADER TRANSFERASE 09-SEP-08 3EFJ TITLE STRUCTURE OF C-MET WITH PYRIMIDONE INHIBITOR 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATOCYTE GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-MET KINASE DOMAIN, UNP RESIDUES 1048-1351; COMPND 5 SYNONYM: HGF RECEPTOR, SCATTER FACTOR RECEPTOR, SF RECEPTOR, HGF/SF COMPND 6 RECEPTOR, MET PROTO-ONCOGENE TYROSINE KINASE, C-MET; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 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: MET; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS C-MET, ALTERNATIVE SPLICING, ATP-BINDING, CHROMOSOMAL REARRANGEMENT, KEYWDS 2 DISEASE MUTATION, GLYCOPROTEIN, KINASE, MEMBRANE, NUCLEOTIDE- KEYWDS 3 BINDING, PHOSPHOPROTEIN, POLYMORPHISM, PROTO-ONCOGENE, RECEPTOR, KEYWDS 4 TRANSFERASE, TRANSMEMBRANE, TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR N.D'ANGELO,S.BELLON,D.WHITTINGTON REVDAT 4 30-AUG-23 3EFJ 1 REMARK REVDAT 3 20-OCT-21 3EFJ 1 REMARK SEQADV REVDAT 2 24-FEB-09 3EFJ 1 VERSN REVDAT 1 07-OCT-08 3EFJ 0 JRNL AUTH N.D.D'ANGELO,S.F.BELLON,S.K.BOOKER,Y.CHENG,A.COXON, JRNL AUTH 2 C.DOMINGUEZ,I.FELLOWS,D.HOFFMAN,R.HUNGATE,P.KAPLAN-LEFKO, JRNL AUTH 3 M.R.LEE,C.LI,L.LIU,E.RAINBEAU,P.J.REIDER,K.REX,A.SIEGMUND, JRNL AUTH 4 Y.SUN,A.S.TASKER,N.XI,S.XU,Y.YANG,Y.ZHANG,T.L.BURGESS, JRNL AUTH 5 I.DUSSAULT,T.S.KIM JRNL TITL DESIGN, SYNTHESIS, AND BIOLOGICAL EVALUATION OF POTENT C-MET JRNL TITL 2 INHIBITORS. JRNL REF J.MED.CHEM. V. 51 5766 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18763753 JRNL DOI 10.1021/JM8006189 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 22426 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) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1527 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.4670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.25000 REMARK 3 B22 (A**2) : -2.53000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : 0.00000 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): 0.648 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.342 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.261 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.267 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4512 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6132 ; 1.080 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 547 ; 4.362 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;37.730 ;23.516 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 739 ;15.728 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;13.754 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 685 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3380 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2120 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3111 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.134 ; 0.200 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): 51 ; 0.162 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.087 ; 0.200 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): 2830 ; 0.512 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4446 ; 0.923 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1978 ; 0.725 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1686 ; 1.154 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3EFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 5.0 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23678 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1R1W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 6000, 1.0M LICL2, 0.1M SODIUM REMARK 280 CITRATE, PH 5.0, VAPOR DIFFUSION, TEMPERATURE 298K 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 37.37050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.62850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.32400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.62850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.37050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.32400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 1047 REMARK 465 GLN A 1048 REMARK 465 ASN A 1049 REMARK 465 THR A 1050 REMARK 465 VAL A 1051 REMARK 465 HIS A 1052 REMARK 465 ILE A 1053 REMARK 465 GLY A 1224 REMARK 465 LEU A 1225 REMARK 465 ALA A 1226 REMARK 465 ARG A 1227 REMARK 465 ASP A 1228 REMARK 465 MET A 1229 REMARK 465 TYR A 1230 REMARK 465 ASP A 1231 REMARK 465 LYS A 1232 REMARK 465 GLU A 1233 REMARK 465 TYR A 1234 REMARK 465 TYR A 1235 REMARK 465 SER A 1236 REMARK 465 VAL A 1237 REMARK 465 HIS A 1238 REMARK 465 ASN A 1239 REMARK 465 LYS A 1240 REMARK 465 THR A 1241 REMARK 465 GLY A 1242 REMARK 465 ALA A 1243 REMARK 465 LYS A 1244 REMARK 465 LEU A 1245 REMARK 465 HIS A 1352 REMARK 465 HIS A 1353 REMARK 465 HIS A 1354 REMARK 465 HIS A 1355 REMARK 465 HIS A 1356 REMARK 465 MET B 1047 REMARK 465 GLN B 1048 REMARK 465 ASN B 1049 REMARK 465 THR B 1050 REMARK 465 VAL B 1051 REMARK 465 HIS B 1052 REMARK 465 ILE B 1053 REMARK 465 PHE B 1223 REMARK 465 GLY B 1224 REMARK 465 LEU B 1225 REMARK 465 ALA B 1226 REMARK 465 ARG B 1227 REMARK 465 ASP B 1228 REMARK 465 MET B 1229 REMARK 465 TYR B 1230 REMARK 465 ASP B 1231 REMARK 465 LYS B 1232 REMARK 465 GLU B 1233 REMARK 465 TYR B 1234 REMARK 465 TYR B 1235 REMARK 465 SER B 1236 REMARK 465 VAL B 1237 REMARK 465 HIS B 1238 REMARK 465 ASN B 1239 REMARK 465 LYS B 1240 REMARK 465 THR B 1241 REMARK 465 GLY B 1242 REMARK 465 ALA B 1243 REMARK 465 LYS B 1244 REMARK 465 LEU B 1245 REMARK 465 HIS B 1352 REMARK 465 HIS B 1353 REMARK 465 HIS B 1354 REMARK 465 HIS B 1355 REMARK 465 HIS B 1356 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 GLN A1064 CG CD OE1 NE2 REMARK 470 ARG A1086 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1114 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1150 CG CD OE1 OE2 REMARK 470 LYS A1259 CG CD CE NZ REMARK 470 LYS A1323 CG CD CE NZ REMARK 470 HIS A1351 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B1064 CG CD OE1 NE2 REMARK 470 ASN B1100 CG OD1 ND2 REMARK 470 ASP B1101 CG OD1 OD2 REMARK 470 ARG B1114 CG CD NE CZ NH1 NH2 REMARK 470 GLU B1127 CG CD OE1 OE2 REMARK 470 GLU B1150 CG CD OE1 OE2 REMARK 470 LYS B1199 CG CD CE NZ REMARK 470 LYS B1259 CG CD CE NZ REMARK 470 LYS B1323 CG CD CE NZ 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 A1055 -93.33 -70.35 REMARK 500 ALA A1057 52.26 -96.03 REMARK 500 ARG A1114 -40.80 176.41 REMARK 500 THR A1116 -72.83 -154.36 REMARK 500 HIS A1136 139.99 -170.24 REMARK 500 ARG A1203 -13.58 77.81 REMARK 500 ASP A1204 41.25 -147.94 REMARK 500 SER B1056 76.99 -63.98 REMARK 500 HIS B1088 -57.11 58.77 REMARK 500 THR B1116 -66.62 -134.93 REMARK 500 ARG B1203 -19.12 82.76 REMARK 500 ASP B1204 55.48 -146.73 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 MT3 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MT3 B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EFK RELATED DB: PDB REMARK 900 STRUCTURE OF C-MET WITH PYRIMIDONE INHIBITOR 50 DBREF 3EFJ A 1048 1351 UNP P08581 MET_HUMAN 1048 1351 DBREF 3EFJ B 1048 1351 UNP P08581 MET_HUMAN 1048 1351 SEQADV 3EFJ MET A 1047 UNP P08581 INITIATING METHIONINE SEQADV 3EFJ LEU A 1272 UNP P08581 VAL 1272 ENGINEERED MUTATION SEQADV 3EFJ HIS A 1352 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS A 1353 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS A 1354 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS A 1355 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS A 1356 UNP P08581 EXPRESSION TAG SEQADV 3EFJ MET B 1047 UNP P08581 INITIATING METHIONINE SEQADV 3EFJ LEU B 1272 UNP P08581 VAL 1272 ENGINEERED MUTATION SEQADV 3EFJ HIS B 1352 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS B 1353 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS B 1354 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS B 1355 UNP P08581 EXPRESSION TAG SEQADV 3EFJ HIS B 1356 UNP P08581 EXPRESSION TAG SEQRES 1 A 310 MET GLN ASN THR VAL HIS ILE ASP LEU SER ALA LEU ASN SEQRES 2 A 310 PRO GLU LEU VAL GLN ALA VAL GLN HIS VAL VAL ILE GLY SEQRES 3 A 310 PRO SER SER LEU ILE VAL HIS PHE ASN GLU VAL ILE GLY SEQRES 4 A 310 ARG GLY HIS PHE GLY CYS VAL TYR HIS GLY THR LEU LEU SEQRES 5 A 310 ASP ASN ASP GLY LYS LYS ILE HIS CYS ALA VAL LYS SER SEQRES 6 A 310 LEU ASN ARG ILE THR ASP ILE GLY GLU VAL SER GLN PHE SEQRES 7 A 310 LEU THR GLU GLY ILE ILE MET LYS ASP PHE SER HIS PRO SEQRES 8 A 310 ASN VAL LEU SER LEU LEU GLY ILE CYS LEU ARG SER GLU SEQRES 9 A 310 GLY SER PRO LEU VAL VAL LEU PRO TYR MET LYS HIS GLY SEQRES 10 A 310 ASP LEU ARG ASN PHE ILE ARG ASN GLU THR HIS ASN PRO SEQRES 11 A 310 THR VAL LYS ASP LEU ILE GLY PHE GLY LEU GLN VAL ALA SEQRES 12 A 310 LYS GLY MET LYS TYR LEU ALA SER LYS LYS PHE VAL HIS SEQRES 13 A 310 ARG ASP LEU ALA ALA ARG ASN CYS MET LEU ASP GLU LYS SEQRES 14 A 310 PHE THR VAL LYS VAL ALA ASP PHE GLY LEU ALA ARG ASP SEQRES 15 A 310 MET TYR ASP LYS GLU TYR TYR SER VAL HIS ASN LYS THR SEQRES 16 A 310 GLY ALA LYS LEU PRO VAL LYS TRP MET ALA LEU GLU SER SEQRES 17 A 310 LEU GLN THR GLN LYS PHE THR THR LYS SER ASP VAL TRP SEQRES 18 A 310 SER PHE GLY VAL LEU LEU TRP GLU LEU MET THR ARG GLY SEQRES 19 A 310 ALA PRO PRO TYR PRO ASP VAL ASN THR PHE ASP ILE THR SEQRES 20 A 310 VAL TYR LEU LEU GLN GLY ARG ARG LEU LEU GLN PRO GLU SEQRES 21 A 310 TYR CYS PRO ASP PRO LEU TYR GLU VAL MET LEU LYS CYS SEQRES 22 A 310 TRP HIS PRO LYS ALA GLU MET ARG PRO SER PHE SER GLU SEQRES 23 A 310 LEU VAL SER ARG ILE SER ALA ILE PHE SER THR PHE ILE SEQRES 24 A 310 GLY GLU HIS TYR VAL HIS HIS HIS HIS HIS HIS SEQRES 1 B 310 MET GLN ASN THR VAL HIS ILE ASP LEU SER ALA LEU ASN SEQRES 2 B 310 PRO GLU LEU VAL GLN ALA VAL GLN HIS VAL VAL ILE GLY SEQRES 3 B 310 PRO SER SER LEU ILE VAL HIS PHE ASN GLU VAL ILE GLY SEQRES 4 B 310 ARG GLY HIS PHE GLY CYS VAL TYR HIS GLY THR LEU LEU SEQRES 5 B 310 ASP ASN ASP GLY LYS LYS ILE HIS CYS ALA VAL LYS SER SEQRES 6 B 310 LEU ASN ARG ILE THR ASP ILE GLY GLU VAL SER GLN PHE SEQRES 7 B 310 LEU THR GLU GLY ILE ILE MET LYS ASP PHE SER HIS PRO SEQRES 8 B 310 ASN VAL LEU SER LEU LEU GLY ILE CYS LEU ARG SER GLU SEQRES 9 B 310 GLY SER PRO LEU VAL VAL LEU PRO TYR MET LYS HIS GLY SEQRES 10 B 310 ASP LEU ARG ASN PHE ILE ARG ASN GLU THR HIS ASN PRO SEQRES 11 B 310 THR VAL LYS ASP LEU ILE GLY PHE GLY LEU GLN VAL ALA SEQRES 12 B 310 LYS GLY MET LYS TYR LEU ALA SER LYS LYS PHE VAL HIS SEQRES 13 B 310 ARG ASP LEU ALA ALA ARG ASN CYS MET LEU ASP GLU LYS SEQRES 14 B 310 PHE THR VAL LYS VAL ALA ASP PHE GLY LEU ALA ARG ASP SEQRES 15 B 310 MET TYR ASP LYS GLU TYR TYR SER VAL HIS ASN LYS THR SEQRES 16 B 310 GLY ALA LYS LEU PRO VAL LYS TRP MET ALA LEU GLU SER SEQRES 17 B 310 LEU GLN THR GLN LYS PHE THR THR LYS SER ASP VAL TRP SEQRES 18 B 310 SER PHE GLY VAL LEU LEU TRP GLU LEU MET THR ARG GLY SEQRES 19 B 310 ALA PRO PRO TYR PRO ASP VAL ASN THR PHE ASP ILE THR SEQRES 20 B 310 VAL TYR LEU LEU GLN GLY ARG ARG LEU LEU GLN PRO GLU SEQRES 21 B 310 TYR CYS PRO ASP PRO LEU TYR GLU VAL MET LEU LYS CYS SEQRES 22 B 310 TRP HIS PRO LYS ALA GLU MET ARG PRO SER PHE SER GLU SEQRES 23 B 310 LEU VAL SER ARG ILE SER ALA ILE PHE SER THR PHE ILE SEQRES 24 B 310 GLY GLU HIS TYR VAL HIS HIS HIS HIS HIS HIS HET MT3 A 1 37 HET MT3 B 2 37 HETNAM MT3 2-BENZYL-5-{4-[(6,7-DIMETHOXYQUINOLIN-4-YL)OXY]-3- HETNAM 2 MT3 FLUOROPHENYL}-3-METHYLPYRIMIDIN-4(3H)-ONE FORMUL 3 MT3 2(C29 H24 F N3 O4) FORMUL 5 HOH *82(H2 O) HELIX 1 1 ASN A 1059 GLN A 1067 1 9 HELIX 2 2 GLY A 1072 SER A 1074 5 3 HELIX 3 3 ASP A 1117 ASP A 1133 1 17 HELIX 4 4 ASP A 1164 ASN A 1171 1 8 HELIX 5 5 THR A 1177 LYS A 1198 1 22 HELIX 6 6 ALA A 1206 ARG A 1208 5 3 HELIX 7 7 PRO A 1246 MET A 1250 5 5 HELIX 8 8 ALA A 1251 THR A 1257 1 7 HELIX 9 9 THR A 1261 THR A 1278 1 18 HELIX 10 10 ASP A 1291 GLN A 1298 1 8 HELIX 11 11 PRO A 1309 TRP A 1320 1 12 HELIX 12 12 SER A 1329 PHE A 1344 1 16 HELIX 13 13 ASN B 1059 GLN B 1067 1 9 HELIX 14 14 GLY B 1072 SER B 1074 5 3 HELIX 15 15 ASP B 1117 PHE B 1134 1 18 HELIX 16 16 ASP B 1164 ASN B 1171 1 8 HELIX 17 17 THR B 1177 LYS B 1198 1 22 HELIX 18 18 ALA B 1206 ARG B 1208 5 3 HELIX 19 19 PRO B 1246 MET B 1250 5 5 HELIX 20 20 GLU B 1253 GLN B 1258 1 6 HELIX 21 21 THR B 1261 THR B 1278 1 18 HELIX 22 22 ASP B 1291 GLY B 1299 1 9 HELIX 23 23 PRO B 1309 TRP B 1320 1 12 HELIX 24 24 LYS B 1323 ARG B 1327 5 5 HELIX 25 25 SER B 1329 THR B 1343 1 15 SHEET 1 A 5 LEU A1076 GLY A1085 0 SHEET 2 A 5 VAL A1092 LEU A1098 -1 O VAL A1092 N ILE A1084 SHEET 3 A 5 LYS A1104 SER A1111 -1 O VAL A1109 N TYR A1093 SHEET 4 A 5 LEU A1154 PRO A1158 -1 O LEU A1157 N ALA A1108 SHEET 5 A 5 GLY A1144 CYS A1146 -1 N GLY A1144 O VAL A1156 SHEET 1 B 2 CYS A1210 LEU A1212 0 SHEET 2 B 2 VAL A1218 VAL A1220 -1 O LYS A1219 N MET A1211 SHEET 1 C 5 LEU B1076 ARG B1086 0 SHEET 2 C 5 CYS B1091 LEU B1098 -1 O HIS B1094 N HIS B1079 SHEET 3 C 5 LYS B1104 SER B1111 -1 O VAL B1109 N TYR B1093 SHEET 4 C 5 LEU B1154 PRO B1158 -1 O LEU B1157 N ALA B1108 SHEET 5 C 5 GLY B1144 CYS B1146 -1 N CYS B1146 O LEU B1154 SHEET 1 D 2 CYS B1210 LEU B1212 0 SHEET 2 D 2 VAL B1218 VAL B1220 -1 O LYS B1219 N MET B1211 SITE 1 AC1 16 ILE A1084 PHE A1089 VAL A1092 ALA A1108 SITE 2 AC1 16 LYS A1110 PHE A1124 GLU A1127 GLY A1128 SITE 3 AC1 16 MET A1131 LEU A1157 PRO A1158 TYR A1159 SITE 4 AC1 16 MET A1160 GLY A1163 MET A1211 PHE A1223 SITE 1 AC2 15 ILE B1084 PHE B1089 VAL B1092 ALA B1108 SITE 2 AC2 15 LYS B1110 PHE B1124 MET B1131 LEU B1140 SITE 3 AC2 15 LEU B1157 PRO B1158 TYR B1159 MET B1160 SITE 4 AC2 15 GLY B1163 MET B1211 HOH B1371 CRYST1 74.741 78.648 129.257 90.00 90.00 90.00 P 21 21 21 8 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 0.013380 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007737 0.00000