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(-) Description

Title :  CRYSTAL STRUCTURE OF SYK IN COMPLEX WITH COMPOUND 2
 
Authors :  S. Han, J. Chang
Date :  15 Jun 15  (Deposition) - 07 Oct 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Spleen Tyrosine Kinase, Inhibitor, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Lovering, C. Aevazelis, J. Chang, C. Dehnhardt, L. Fitz, S. Han, K. Janz, J. Lee, N. Kaila, J. Mcdonald, W. Moore, A. Moretto, N. Papaioannou, D. Richard, M. S. Ryan, Z. K. Wan, A. Thorarensen
Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified By Free-Energy Perturbation (Fep).
Chemmedchem V. 11 217 2016
PubMed-ID: 26381330  |  Reference-DOI: 10.1002/CMDC.201500333

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE SYK
    Chains: A
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 343-635
    Gene: SYK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPLEEN TYROSINE KINASE,P72-SYK
 
Molecule 2 - GLU-VAL-TYR-GLU-SER
    Chains: D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
150J1Ligand/Ion3-{8-[(3,4-DIMETHOXYPHENYL)AMINO]IMIDAZO[1,2-A]PYRAZIN-6-YL}-N-[4-(METHYLCARBAMOYL)PHENYL]BENZAMIDE
2GOL1Ligand/IonGLYCEROL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:377 , PHE A:382 , ALA A:400 , GLU A:449 , MET A:450 , ALA A:451 , GLU A:452 , GLY A:454 , PRO A:455 , ASN A:457 , LYS A:458 , GLN A:461 , LEU A:501 , HOH A:857 , HOH A:869binding site for residue 50J A 701
2AC2SOFTWAREGLU A:486 , GLY A:618 , PHE A:619 , ALA A:620 , ALA A:621 , HOH A:920 , HOH A:956binding site for residue GOL A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C27)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:410 -Pro A:411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C27)

(-) Exons   (0, 0)

(no "Exon" information available for 5C27)

(-) Sequences/Alignments

Asymmetric/Biological 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee...eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhh........eeeeee...eeeeee....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c27 A 363 VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENyyKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNH 636
                                   372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522  ||   532       542       552       562       572       582       592       602       612       622       632    
                                                                                                                                                                                            525-PTR                                                                                                           
                                                                                                                                                                                             526-PTR                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5c27 D 346 EVYES 350
   Legend:   → Mismatch (orange background)
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    → 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 5C27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C27)

(-) Gene Ontology  (87, 87)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asp A:410 - Pro A:411   [ RasMol ]  
 

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  5c27
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  KSYK_HUMAN | P43405
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  2.7.10.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        KSYK_HUMAN | P43405: 1a81 1csy 1csz 1xba 1xbb 1xbc 3buw 3emg 3fqe 3fqh 3fqs 3srv 3tub 3tuc 3tud 3vf8 3vf9 4dfl 4dfn 4f4p 4fl1 4fl2 4fl3 4fyn 4fyo 4fz6 4fz7 4gfg 4i0r 4i0s 4i0t 4puz 4pv0 4px6 4rss 4rx7 4rx8 4rx9 4wnm 4xg2 4xg3 4xg4 4xg6 4xg7 4xg8 4xg9 4yjo 4yjp 4yjq 4yjr 4yjs 4yjt 4yju 4yjv 5c26 5cxh 5cxz 5cy3 5ghv 5lma 5lmb 5t68 5tiu 5tr6 5tt7

(-) Related Entries Specified in the PDB File

5c26