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(-) Description

Title :  CRYSTAL STRUCTURE OF DYRK2 IN COMPLEX WITH EHT 5372 (COMPOUND 1)
 
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 :  2.15
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, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
17AA2Ligand/IonMETHYL 9-[(2,4-DICHLOROPHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
17AA1Ligand/IonMETHYL 9-[(2,4-DICHLOROPHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
17AA1Ligand/IonMETHYL 9-[(2,4-DICHLOROPHENYL)AMINO]-[1,3]THIAZOLO[5,4-F]QUINAZOLINE-2-CARBOXIMIDATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:155 , GLY A:156 , LYS A:157 , VAL A:163 , ALA A:176 , LYS A:178 , ILE A:212 , PHE A:228 , GLU A:229 , LEU A:231 , SER A:232 , ASN A:234 , GLU A:279 , LEU A:282 , ILE A:294 , EDO A:504binding site for residue 7AA A 501
02AC2SOFTWARELYS A:165 , HOH A:654binding site for residue EDO A 502
03AC3SOFTWAREGLU A:363 , LYS A:413 , ARG A:415binding site for residue EDO A 503
04AC4SOFTWAREILE A:155 , SER A:232 , MET A:233 , ASN A:234 , 7AA A:501 , HOH A:699 , HOH A:710binding site for residue EDO A 504
05AC5SOFTWAREHIS A:199 , LYS A:202 , ASP B:437 , GLN B:441binding site for residue EDO A 506
06AC6SOFTWARELYS A:254binding site for residue EDO A 507
07AC7SOFTWAREPRO A:350 , LYS A:413 , ARG A:415 , ARG B:411binding site for residue EDO A 508
08AC8SOFTWARESER A:104 , TYR A:105 , HOH A:633binding site for residue EDO A 509
09AC9SOFTWAREILE B:155 , GLY 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 , GLU B:279 , LEU B:282 , ILE B:294 , ASP B:295 , HOH B:673binding site for residue 7AA B 501
10AD1SOFTWARELYS A:202 , LEU B:436 , LYS B:440 , HOH B:646 , HOH B:719binding site for residue EDO B 502
11AD2SOFTWARELYS B:277 , GLU B:279 , SER B:312 , HOH B:605 , HOH B:643binding site for residue EDO B 503
12AD3SOFTWARELYS B:386 , TYR B:388binding site for residue EDO B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LXC)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh.............ee...eeeeeeeeee..eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.......eee......ee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhh.........eeee.....eeee.ee.....ee......hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lxc A  80 PMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTyIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLR 463
                                    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..................hhhhhh..............ee...eeeeeeeeee..eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeee.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eee.......eee......ee..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh..hhhhhh.........eeee.....eeee.ee.....ee......hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxc 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 5LXC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

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

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