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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF JANUS KINASE 2 IN COMPLEX WITH N,N-DICYCLOPROPYL-10-ETHYL-7-[(3-METHOXYPROPYL)AMINO] -3-METHYL-3,5,8,10-TETRAAZATRICYCLO[7.3.0.0,6] DODECA-1(9),2(6),4,7,11-PENTAENE-11-CARBOXAMIDE
 
Authors :  J. S. Sack
Date :  08 Jul 15  (Deposition) - 26 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wan, G. M. Schroeder, A. C. Hart, J. Inghrim, J. Grebinski, J. S. Tokarski, M. V. Lorenzi, D. You, T. Mcdevitt, B. Penhallow, R. Vuppugalla, Y. Zhang, X. Gu, R. Iyer, L. J. Lombardo, G. L. Trainor, S. Ruepp, J. Lippy, Y. Blat, J. S. Sack, J. A. Khan, K. Stefanski, B. Sleczka, A. Mathur, J. H. Sun, M. K. Wong, D. R. Wu, P. Li, A. Gupta, P. N. Arunachalam, B. Pragalathan, S. Narayanan, N. K C, P. Kuppusamy A. V. Purandare
Discovery Of A Highly Selective Jak2 Inhibitor, Bms-911543, For The Treatment Of Myeloproliferative Neoplasms.
Acs Med. Chem. Lett. V. 6 850 2015
PubMed-ID: 26288683  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00226

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE JAK2
    Chains: A, B
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 839-1132
    Gene: JAK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JANUS KINASE 2,JAK-2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
150V2Ligand/IonN,N-DICYCLOPROPYL-4-[(1,5-DIMETHYL-1H-PYRAZOL-3-YL)AMINO]-6-ETHYL-1-METHYL-1,6-DIHYDROIMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDINE-7-CARBOXAMIDE
2PTR4Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
150V1Ligand/IonN,N-DICYCLOPROPYL-4-[(1,5-DIMETHYL-1H-PYRAZOL-3-YL)AMINO]-6-ETHYL-1-METHYL-1,6-DIHYDROIMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDINE-7-CARBOXAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
150V1Ligand/IonN,N-DICYCLOPROPYL-4-[(1,5-DIMETHYL-1H-PYRAZOL-3-YL)AMINO]-6-ETHYL-1-METHYL-1,6-DIHYDROIMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDINE-7-CARBOXAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:855 , GLY A:856 , LYS A:857 , GLY A:858 , VAL A:863 , ALA A:880 , GLU A:930 , TYR A:931 , LEU A:932 , PRO A:933 , GLY A:935 , ARG A:980 , ASN A:981 , LEU A:983 , ASP A:994 , HOH A:4158 , GLU B:987binding site for residue 50V A 4000
2AC2SOFTWARELEU B:855 , GLY B:856 , ALA B:880 , GLU B:930 , TYR B:931 , LEU B:932 , PRO B:933 , GLY B:935 , ARG B:980 , ASN B:981 , LEU B:983 , ASP B:994 , HOH B:4266binding site for residue 50V B 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CF8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CF8)

(-) Exons   (0, 0)

(no "Exon" information available for 5CF8)

(-) 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:287
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee.........eeeeeee...hhhhhhhhhhhhhhhhh........eeeee...eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cf8 A  842 TQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEyyKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGH 1133
                                   851       861       871       881       891       901       911      |926       936       946       956       966       976       986       996      1006||    1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126       
                                                                                                      918|                                                                               1007-PTR                                                                                                                          
                                                                                                       924                                                                                1008-PTR                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhh.eeeeeeeee...eeeeeeee.........eeeeeee...hhhhhhhhhhhhhhhhh........eeeee...eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cf8 B  839 RDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEyyKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGH 1133
                                   848       858       868       878       888       898       908       918|      933       943       953       963       973       983       993      1003   || 1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133
                                                                                                         918|                                                                               1007-PTR                                                                                                                          
                                                                                                          924                                                                                1008-PTR
   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 5CF8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CF8)

(-) Gene Ontology  (114, 114)

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
    50V  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cf8)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  5cf8
    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
  JAK2_HUMAN | O60674
    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
  JAK2_HUMAN | O60674
    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
        JAK2_HUMAN | O60674: 2b7a 2w1i 2xa4 3e62 3e63 3e64 3fup 3io7 3iok 3jy9 3kck 3krr 3lpb 3q32 3rvg 3tjc 3tjd 3ugc 3zmm 4aqc 4bbe 4bbf 4c61 4c62 4d0w 4d0x 4d1s 4e4m 4e6d 4e6q 4f08 4f09 4fvp 4fvq 4fvr 4gfm 4gmy 4hge 4iva 4ji9 4jia 4p7e 4ytc 4ytf 4yth 4yti 4z32 4zim 5aep 5cf4 5cf5 5cf6 5hez 5i4n 5l3a 5tq3 5tq4 5tq5 5tq6 5tq7 5tq8 5usy 5usz 5ut0 5ut1 5ut2 5ut3 5ut4 5ut5 5ut6

(-) Related Entries Specified in the PDB File

5cf4 5cf5 5cf6