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(-) Description

Title :  CRYSTAL STRUCTURE OF DYRK2 IN COMPLEX WITH EHT 1610 (COMPOUND 2)
 
Authors :  A. Chaikuad, F. Von Delft, C. H. Arrowsmith, A. Edwards, C. Bountra, T. S. Knapp, Structural Genomics Consortium (Sgc)
Date :  20 Sep 16  (Deposition) - 26 Oct 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Kinase, Inhibitor, Unusual Binding Mode, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, J. Diharce, M. Schroder, A. Foucourt, B. Leblond, A. S. Casagrande, L. Desire, P. Bonnet, S. Knapp, T. Besson
An Unusual Binding Model Of The Methyl 9-Anilinothiazolo[5, 4-F] Quinazoline-2-Carbimidates (Eht 1610 And Eht 5372) Confers High Selectivity For Dual-Specificity Tyrosine Phosphorylation-Regulated Kinases
J. Med. Chem. V. 59 10315 2016
PubMed-ID: 27766861  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01083

(-) Compounds

Molecule 1 - DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 2
    Chains: A, B
    EC Number: 2.7.12.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector Type: PLASMID
    Gene: DYRK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
17A72Ligand/IonMETHYL 9-[(2-FLUORANYL-4-METHOXY-PHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
17A71Ligand/IonMETHYL 9-[(2-FLUORANYL-4-METHOXY-PHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
17A71Ligand/IonMETHYL 9-[(2-FLUORANYL-4-METHOXY-PHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:156 , LYS A:157 , PHE A:160 , VAL A:163 , ALA A:176 , LYS A:178 , ILE A:212 , PHE A:228 , GLU A:229 , LEU A:231 , LEU A:282 , ILE A:294 , ASP A:295binding site for residue 7A7 A 501
02AC2SOFTWAREASN A:381binding site for residue EDO A 502
03AC3SOFTWAREARG A:421 , ASN A:425binding site for residue EDO A 503
04AC4SOFTWAREARG A:458binding site for residue EDO A 504
05AC5SOFTWAREARG A:288 , GLY A:290binding site for residue EDO A 505
06AC6SOFTWARESER A:384 , SER A:385 , ARG A:390binding site for residue EDO A 506
07AC7SOFTWAREGLY B:156 , LYS B:157 , PHE B:160 , VAL B:163 , ALA B:176 , LYS B:178 , ILE B:212 , PHE B:228 , GLU B:229 , LEU B:231 , ASN B:280 , LEU B:282 , ILE B:294 , ASP B:295binding site for residue 7A7 B 501
08AC8SOFTWARETHR B:308binding site for residue EDO B 502
09AC9SOFTWAREARG B:378 , ASN B:381binding site for residue EDO B 503
10AD1SOFTWAREARG B:421 , ASN B:425 , HOH B:642binding site for residue EDO B 504
11AD2SOFTWAREARG B:288 , GLY B:290binding site for residue EDO B 505
12AD3SOFTWARESER B:384 , SER B:385 , ARG B:390binding site for residue EDO B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LXD)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh.............ee...eeeeeeeeee..eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.......eee......ee..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhh.........eeee.....eeee.ee.....ee......hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxd A  80 PMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTyIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR 465
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459      
                                                                                                                                                                                                                                                               309-PTR                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh.............ee...eeeeeeeeee..eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.......eee......ee..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhh.........eeee.....eeee.ee.....ee......hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxd B  80 PMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTyIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR 465
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459      
                                                                                                                                                                                                                                                               309-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 5LXD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

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        DYRK2_HUMAN | Q92630: 3k2l 3kvw 4azf 5lxc

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