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(-) Description

Title :  CRYSTAL STRUCTURE OF PTK6 KINASE DOMAIN COMPLEXED WITH DASATINIB
 
Authors :  M. K. Thakur, S. Birudukota, S. Swaminathan, R. Tyagi, R. Gosu
Date :  18 Oct 16  (Deposition) - 04 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase, Kinase, Brk, Ptk6, Dasatinib (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Thakur, S. Birudukota, S. Swaminathan, S. K. Battula, S. Vadivelu, R. Tyagi, R. Gosu
Co-Crystal Structures Of Ptk6: With Dasatinib At 2. 24 Angstrom , With Novel Imidazo[1, 2-A]Pyrazin-8-Amine Derivative Inhibitor At 1. 70 Angstrom Resolution
Biochem. Biophys. Res. V. 482 1289 2017 Commun.
PubMed-ID: 27993680  |  Reference-DOI: 10.1016/J.BBRC.2016.12.030

(-) Compounds

Molecule 1 - PROTEIN-TYROSINE KINASE 6
    Chains: A, B, C, D
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN, UNP RESIDUES 185-446
    Gene: PTK6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BREAST TUMOR KINASE,TYROSINE-PROTEIN KINASE BRK

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
11N14Ligand/IonN-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
2CXM4Mod. Amino AcidN-CARBOXYMETHIONINE
3GOL12Ligand/IonGLYCEROL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
11N11Ligand/IonN-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
2CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
3GOL3Ligand/IonGLYCEROL
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
11N11Ligand/IonN-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
2CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
3GOL3Ligand/IonGLYCEROL
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
11N11Ligand/IonN-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
2CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
3GOL3Ligand/IonGLYCEROL
Biological Unit 4 (3, 5)
No.NameCountTypeFull Name
11N11Ligand/IonN-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
2CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
3GOL3Ligand/IonGLYCEROL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:197 , VAL A:205 , ALA A:217 , ILE A:218 , LYS A:219 , LEU A:248 , ILE A:262 , THR A:264 , LEU A:266 , MET A:267 , ALA A:268 , GLY A:270 , LEU A:319 , GLY A:329 , ASP A:330 , HOH A:612 , HOH A:688binding site for residue 1N1 A 501
02AC2SOFTWAREASP A:312 , ARG A:316 , TYR A:342 , HIS A:345 , TRP A:353 , HOH A:602 , HOH A:658binding site for residue GOL A 502
03AC3SOFTWAREARG A:311 , ALA A:334 , ILE A:337 , GLU A:339 , TYR A:364binding site for residue GOL A 503
04AC4SOFTWAREGLU A:235 , TYR A:308 , ILE A:309 , ARG A:311 , GLY A:332binding site for residue GOL A 504
05AC5SOFTWARELEU B:197 , VAL B:205 , ALA B:217 , ILE B:218 , LYS B:219 , LEU B:248 , ILE B:262 , THR B:264 , LEU B:266 , MET B:267 , ALA B:268 , GLY B:270 , GLY B:329 , ASP B:330 , HOH B:684 , HOH B:703binding site for residue 1N1 B 501
06AC6SOFTWAREASP B:312 , ARG B:316 , HIS B:345 , TRP B:353 , HOH B:601 , HOH B:613 , HOH B:622binding site for residue GOL B 502
07AC7SOFTWAREARG B:311 , ALA B:334 , ARG B:335 , TYR B:364 , HOH B:606binding site for residue GOL B 503
08AC8SOFTWAREGLU B:235 , TYR B:308 , ILE B:309 , ARG B:311 , GLY B:332 , ARG B:335 , HOH B:679binding site for residue GOL B 504
09AC9SOFTWAREALA C:217 , LYS C:219 , ILE C:262 , THR C:264 , MET C:267 , ALA C:268 , LYS C:269 , GLY C:270 , GLU C:274 , ASP C:330 , HOH C:643binding site for residue 1N1 C 501
10AD1SOFTWAREASP C:312 , ARG C:316 , HIS C:345 , TRP C:353 , HOH C:605 , HOH C:649 , HOH C:652binding site for residue GOL C 502
11AD2SOFTWAREARG C:311 , ALA C:334 , ILE C:337 , GLU C:339 , TYR C:364binding site for residue GOL C 503
12AD3SOFTWAREGLU C:235 , ASN C:307 , TYR C:308 , ILE C:309 , ARG C:311 , GLY C:332binding site for residue GOL C 504
13AD4SOFTWAREASP D:312 , ARG D:316 , TYR D:342 , HIS D:345 , PRO D:350 , TRP D:353 , HOH D:638 , HOH D:668 , HOH D:694binding site for residue GOL D 501
14AD5SOFTWAREARG D:311 , ALA D:334 , ILE D:337 , GLU D:339 , TYR D:342 , TYR D:364 , HOH D:606binding site for residue GOL D 502
15AD6SOFTWAREGLU D:235 , TYR D:308 , ILE D:309 , ARG D:311 , GLY D:332 , ARG D:335binding site for residue GOL D 503
16AD7SOFTWARELEU D:197 , VAL D:205 , ALA D:217 , LYS D:219 , LEU D:248 , ILE D:262 , THR D:264 , MET D:267 , ALA D:268 , GLY D:270 , ASP D:330 , HOH D:656 , HOH D:685 , HOH D:705binding site for residue 1N1 D 504
17AD8SOFTWAREARG B:186 , LYS B:240 , TYR B:251 , ALA B:252 , VAL B:253 , VAL B:254 , SER B:255 , HOH B:609 , HOH B:624 , HOH B:646 , HOH B:674 , LEU D:410 , GLU D:411binding site for Di-peptide CXM B 184 and GLU B 185
18AD9SOFTWAREGLU A:411 , ARG C:186 , LYS C:240 , TYR C:251 , ALA C:252 , VAL C:253 , SER C:255 , HOH C:620 , HOH C:678binding site for Di-peptide CXM C 184 and GLU C 185
19AE1SOFTWAREARG D:186 , LYS D:240 , TYR D:251 , ALA D:252 , VAL D:253 , VAL D:254 , SER D:255 , HOH D:617 , HOH D:658 , HOH D:669 , HOH D:698binding site for Di-peptide CXM D 184 and GLU D 185

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H2U)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:258 -Pro A:259
2Asp B:258 -Pro B:259
3Asp C:258 -Pro C:259
4Asp D:258 -Pro D:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H2U)

(-) Exons   (0, 0)

(no "Exon" information available for 5H2U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee...eeeeeeeehhhhh.hhhhhhhhhhhhhh..........eee.....eeeeee....eehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhh.hhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h2u A 184 mERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPTFKALRERLSSFTSHHHH 450
                            |      193       203       213       223       233       243       253       263       273   ||  284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444      
                            |                                                                                          277|                                                                                                                                                                           
                          184-CXM                                                                                       279                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee...eeeeeeeehhhhh.hhhhhhhhhhhhhhh.........eee.....eeeeee....eehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h2u B 184 mERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPTFKALRERLSSFTSHH 448
                            |      193       203       213       223       233       243       253       263       273   ||  284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
                          184-CXM                                                                                      277|                                                                                                                                                                         
                                                                                                                        279                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee...eeeeeeeehhhhh.hhhhhhhhhhhhhhh.........eee.....eeeeee....eehhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h2u C 184 mERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPTFKALRERLSSFTSHHH 449
                            |      193       203       213       223       233       243       253       263       273   ||  284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
                          184-CXM                                                                                      277|                                                                                                                                                                          
                                                                                                                        279                                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee...eeeeeeeehhhhh.hhhhhhhhhhhhh...........eee.....eeeeee.....hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h2u D 184 mERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPTFKALRERLSSFTSHH 448
                            |      193       203       213       223       233       243       253       263       273   ||  284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
                          184-CXM                                                                                      277|                                                                                                                                                                         
                                                                                                                        279
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5H2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H2U)

(-) Gene Ontology  (35, 35)

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  5h2u
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  PTK6_HUMAN | Q13882
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 Related Entries

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        PTK6_HUMAN | Q13882: 1rja 2kgt 5d7v 5da3

(-) Related Entries Specified in the PDB File

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