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(-) Description

Title :  HUMAN SPLEEN TYROSINE KINASE KINASE DOMAIN IN COMPLEX WITH AZANAPHTHYRIDINE INHIBITOR
 
Authors :  D. O. Somers, M. Neu
Date :  29 Jul 16  (Deposition) - 14 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Complex, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. S. Garton, M. D. Barker, R. P. Davis, C. Douault, E. Hooper-Greenhill, E. Jones, H. D. Lewis, J. Liddle, D. Lugo, S. Mccleary, A. G. Preston, C. Ramirez-Molina, M. Neu, T. J. Shipley, D. O. Somers, R. J. Watson, D. M. Wilson
Optimisation Of A Novel Series Of Potent And Orally Bioavailable Azanaphthyridine Syk Inhibitors.
Bioorg. Med. Chem. Lett. V. 26 4606 2016
PubMed-ID: 27578246  |  Reference-DOI: 10.1016/J.BMCL.2016.08.070

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE SYK
    Chains: A, B
    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-HM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 360-635
    Gene: SYK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPLEEN TYROSINE KINASE,P72-SYK

 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  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
16ZF2Ligand/Ion7-[6-(DIMETHYLAMINO)PYRIDIN-3-YL]-~{N}-[[(3~{S})-PIPERIDIN-3-YL]METHYL]PYRIDO[3,4-B]PYRAZIN-5-AMINE
2GOL7Ligand/IonGLYCEROL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
16ZF1Ligand/Ion7-[6-(DIMETHYLAMINO)PYRIDIN-3-YL]-~{N}-[[(3~{S})-PIPERIDIN-3-YL]METHYL]PYRIDO[3,4-B]PYRAZIN-5-AMINE
2GOL5Ligand/IonGLYCEROL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
16ZF1Ligand/Ion7-[6-(DIMETHYLAMINO)PYRIDIN-3-YL]-~{N}-[[(3~{S})-PIPERIDIN-3-YL]METHYL]PYRIDO[3,4-B]PYRAZIN-5-AMINE
2GOL2Ligand/IonGLYCEROL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:377 , VAL A:385 , ALA A:400 , GLU A:449 , MET A:450 , ALA A:451 , GLU A:452 , GLY A:454 , PRO A:455 , ARG A:498 , ASN A:499 , LEU A:501 , ASP A:512 , HOH A:845 , HOH A:889binding site for residue 6ZF A 701
2AC2SOFTWARELEU A:377 , LYS A:387 , MET A:450 , GLU A:452 , THR B:610 , ASN B:615binding site for residue GOL A 702
3AC3SOFTWARELEU A:585 , GLU A:586 , TYR A:611 , HOH A:811 , HOH A:932 , HOH A:958 , VAL B:503 , THR B:504 , HOH B:825binding site for residue GOL A 703
4AC4SOFTWARETYR A:431 , TYR A:507 , HOH A:847 , HOH A:931binding site for residue GOL A 704
5AC5SOFTWAREARG A:498binding site for residue GOL A 706
6AC6SOFTWARELEU B:377 , VAL B:385 , ALA B:400 , GLU B:449 , MET B:450 , ALA B:451 , GLU B:452 , GLY B:454 , PRO B:455 , ARG B:498 , ASN B:499 , LEU B:501 , ASP B:512 , HOH B:807 , HOH B:857binding site for residue 6ZF B 701
7AC7SOFTWARELEU A:453 , VAL A:503 , HOH A:843 , LEU B:585 , GLU B:586 , TYR B:611 , HOH B:913binding site for residue GOL B 702
8AC8SOFTWARETYR B:431 , HOH B:835binding site for residue GOL B 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LMB)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeee....eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lmb A 364 YLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENyYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVV 634
                                   373       383       393       403||     419       429       439       449       459       469       479       489       499       509       519     | 529       539       549       559       569       579       589       599       609       619       629     
                                                                  404|                                                                                                               525-PTR                                                                                                         
                                                                   411                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeeee..eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee..hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.eee......hhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lmb B 364 YLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENyYKAWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYY 630
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523 |  || 538       548       558       568       578       588       598       608       618       628  
                                                                                                                                                                                           525-PTR                                                                                                
                                                                                                                                                                                              528|                                                                                                
                                                                                                                                                                                               534
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  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 5LMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (87, 87)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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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 5c27 5cxh 5cxz 5cy3 5ghv 5lma 5t68 5tiu 5tr6 5tt7

(-) Related Entries Specified in the PDB File

5lma