Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE JAK3 KINASE DOMAIN COVALENTLY BOUND TO N-(3-(((5-CHLORO-2-((2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL)AMINO) PYRIMIDIN-4-YL)AMINO)METHYL)PHENYL)ACRYLAMIDE
 
Authors :  R. Mcnally, L. Tan, N. S. Gray, M. J. Eck
Date :  26 Mar 15  (Deposition) - 10 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
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 :  Tyrosine Kinase, Kinase Domain, Covalent Inhibitor Complex, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tan, K. Akahane, R. Mcnally, K. M. Reyskens, S. B. Ficarro, S. Liu, G. S. Herter-Sprie, S. Koyama, M. J. Pattison, K. Labella, L. Johannessen, E. A. Akbay, K. K. Wong, D. A. Frank, J. A. Marto, T. A. Look, J. S. Arthur, M. J. Eck, N. S. Gray
Development Of Selective Covalent Janus Kinase 3 Inhibitors
J. Med. Chem. V. 58 6589 2015
PubMed-ID: 26258521  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00710

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE JAK3
    Chains: A, B, C, D
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 811-1124
    Gene: JAK3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JANUS KINASE 3,JAK-3,LEUKOCYTE JANUS KINASE,L-JAK

 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  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
14LH4Ligand/IonN-(3-{[(5-CHLORO-2-{[2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]METHYL}PHENYL)PROP-2-ENAMIDE
2PTR8Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
14LH1Ligand/IonN-(3-{[(5-CHLORO-2-{[2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]METHYL}PHENYL)PROP-2-ENAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
14LH1Ligand/IonN-(3-{[(5-CHLORO-2-{[2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]METHYL}PHENYL)PROP-2-ENAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
14LH1Ligand/IonN-(3-{[(5-CHLORO-2-{[2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]METHYL}PHENYL)PROP-2-ENAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
14LH1Ligand/IonN-(3-{[(5-CHLORO-2-{[2-METHOXY-4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}PYRIMIDIN-4-YL)AMINO]METHYL}PHENYL)PROP-2-ENAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:828 , VAL A:836 , ALA A:853 , MET A:902 , GLU A:903 , TYR A:904 , LEU A:905 , PRO A:906 , GLY A:908 , CYS A:909 , ARG A:911 , ASP A:912 , ARG A:953 , LEU A:956 , ALA A:966binding site for residue 4LH A 2000
2AC2SOFTWARELEU B:828 , VAL B:836 , ALA B:853 , MET B:902 , GLU B:903 , TYR B:904 , LEU B:905 , PRO B:906 , GLY B:908 , LEU B:910 , ARG B:911 , ASP B:912 , PHE B:913 , ARG B:953 , ILE B:955 , LEU B:956 , ALA B:966binding site for residue 4LH B 2000
3AC3SOFTWARELEU C:828 , VAL C:836 , ALA C:853 , MET C:902 , GLU C:903 , TYR C:904 , LEU C:905 , PRO C:906 , GLY C:908 , LEU C:910 , ARG C:911 , ASP C:912 , PHE C:913 , ARG C:953 , ILE C:955 , LEU C:956 , ALA C:966binding site for residue 4LH C 2000
4AC4SOFTWARELEU D:828 , VAL D:836 , ALA D:853 , MET D:902 , GLU D:903 , TYR D:904 , LEU D:905 , PRO D:906 , GLY D:908 , LEU D:910 , ARG D:911 , ASP D:912 , PHE D:913 , ARG D:953 , ILE D:955 , LEU D:956 , ALA D:966binding site for residue 4LH D 2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z16)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z16)

(-) 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:273
                                                                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee....eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee...eeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhhheeehhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z16 A  814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYELRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDyyVVRPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR 1103
                                   823       833       843       853       863       873       883       898       908       918       928       938       948       958       968       978 ||  ||993      1003      1013      1023      1033    ||1050      1060      1070      1080      1090      1100   
                                                                                                       891|                                                                                980-PTR|                                            1038|                                                         
                                                                                                        897                                                                                 981-PTR                                             1046                                                         
                                                                                                                                                                                               984|                                                                                                          
                                                                                                                                                                                                990                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee....eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee...eeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee............hhhhhhhheeehhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z16 B  814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYELRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDyyVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR 1103
                                   823       833       843       853       863       873       883       898       908       918       928       938       948       958       968       978 ||    988       998      1008      1018      1028      1038|     1055      1065      1075      1085      1095        
                                                                                                       891|                                                                                980-PTR                                                  1038|                                                         
                                                                                                        897                                                                                 981-PTR                                                  1046                                                         


Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee....eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee...eeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhh.eeehhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z16 C  814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYELRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDyyVVRPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR 1103
                                   823       833       843       853       863       873       883       898       908       918       928       938       948       958       968       978 ||  ||993      1003      1013      1023      1033    ||1050      1060      1070      1080      1090      1100   
                                                                                                       891|                                                                                980-PTR|                                            1038|                                                         
                                                                                                        897                                                                                 981-PTR                                             1046                                                         
                                                                                                                                                                                               984|                                                                                                          
                                                                                                                                                                                                990                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeee....eeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh.......eeeee...eeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhh.eeehhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z16 D  814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYELRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDyyVVRPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR 1103
                                   823       833       843       853       863       873       883       898       908       918       928       938       948       958       968       978 ||  ||993      1003      1013      1023      1033    ||1050      1060      1070      1080      1090      1100   
                                                                                                       891|                                                                                980-PTR|                                            1038|                                                         
                                                                                                        897                                                                                 981-PTR                                             1046                                                         
                                                                                                                                                                                               984|                                                                                                          
                                                                                                                                                                                                990
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4Z16)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z16)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z16)

(-) Gene Ontology  (54, 54)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4LH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4z16)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4z16
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  JAK3_HUMAN | P52333
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  JAK3_HUMAN | P52333
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        JAK3_HUMAN | P52333: 1yvj 3lxk 3lxl 3pjc 3zc6 3zep 4hvd 4hvg 4hvh 4hvi 4i6q 4qps 4qt1 4rio 4v0g 5lwm 5lwn 5toz 5tts 5ttu 5ttv 5vo6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Z16)