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(-) Description

Title :  CRYSTAL STRUCTURE OF IRAK4 IN COMPLEX WITH COMPOUND 11
 
Authors :  S. Han, J. S. Chang
Date :  14 Jan 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Irak4, Kinase, Fragment Screening (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Lee, C. M. Ambler, D. R. Anderson, B. P. Boscoe, A. G. Bree, J. I. Brodfuehrer, J. S. Chang, C. Choi, S. W. Chung, K. J. Curran, J. E. Day, C. M. Dehnhardt, K. Dower, S. E. Drozda, R. K. Frisbie, L. K. Gavrin, J. A. Goldberg, S. Han, M. Hegen, D. Hepworth, H. R. Hope, S. Kamtekar, I. C. Kilty, A. Lee, L. L. Lin, F. E. Lovering, M. D. Lowe, J. P. Mathias, H. M. Morgan, E. A. Murphy, N. Papaioannou, A. Patny, B. S. Pierce, V. R. Rao, E. Saiah, I. J. Samardjiev, B. M. Samas, M. W. H. Shen, J. H. Shin, H. H. Soutter, J. W. Strohbach, P. T. Symanowicz, J. R. Thomason, J. D. Trzupek, R. Vargas, F. Vincent, J. Yan, C. W. Zapf, S. W. Wright
Discovery Of Clinical Candidate 1-{[(2S, 3S, 4S) -3-Ethyl-4-Fluoro-5-Oxopyrrolidin-2-Yl]Methoxy}-7-Methoxyis Quinoline-6-Carboxamide (Pf-06650833), A Potent, Selective Inhibitor Of Interleukin-1 Receptor Associated Kinase 4 (Irak4), By Fragment-Based Drug Design.
J. Med. Chem. 2017
PubMed-ID: 28498658  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00231

(-) Compounds

Molecule 1 - INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 154-460
    Gene: IRAK4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IRAK-4,RENAL CARCINOMA ANTIGEN NY-REN-64

 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
18BY2Ligand/Ion5-(4-CYANOPHENYL)-3-[(PROPAN-2-YL)OXY]NAPHTHALENE-2-CARBOXAMIDE
2SEP2Mod. Amino AcidPHOSPHOSERINE
3TPO3Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
18BY1Ligand/Ion5-(4-CYANOPHENYL)-3-[(PROPAN-2-YL)OXY]NAPHTHALENE-2-CARBOXAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
18BY1Ligand/Ion5-(4-CYANOPHENYL)-3-[(PROPAN-2-YL)OXY]NAPHTHALENE-2-CARBOXAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:194 , VAL A:200 , ALA A:211 , TYR A:262 , VAL A:263 , TYR A:264 , MET A:265 , GLY A:268 , LYS A:313 , ALA A:315 , LEU A:318binding site for residue 8BY A 800
2AC2SOFTWAREMET B:192 , GLU B:194 , GLY B:196 , ALA B:211 , TYR B:262 , VAL B:263 , TYR B:264 , MET B:265 , LYS B:313 , ALA B:315 , LEU B:318binding site for residue 8BY B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:392 -Pro A:393
2Glu B:392 -Pro B:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UIR)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh.........eeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhh.......eeeee..eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uir A 165 FHSFSFYELKNVTNNFDERPGNKMGEGGFGVVYKGYVNNTTVAVKKLADITTEELKQQFDQEIKVMAKCQHENLVELLGFSDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174       184|      198       208       221       231       241       251||     265       275       285       295       305       315       325       335|||    353       363       373       383       393       403  ||   416       426       436       446       456  
                                             184|                        216|                             252|                                                                           335|||                                                         406|                                                
                                              189                         220                              257                                                                            344||                                                          410                                                
                                                                                                                                                                                           345-TPO                                                                                                          
                                                                                                                                                                                            346-SEP                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhh..........eeee...eeee......eeeeee...hhhhhhhhhhhhhhhh.......eeeee....eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee......hhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uir B 164 RFHSFSFYELKNVTNNFDERPIGNKMGEGGFGVVYKGYVTTVAVKKLAAEELKQQFDQEIKVMAKCQHENLVELLGFSSDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   173       183 ||    196       208       224       234       244       254|      266       276       286       296       306       316       326       336|  ||  351       361       371       381       391       401    || 412       422       432       442       452      
                                               185|             205|      217|                           254|                                                                            336|  ||                                                         406|                                                  
                                                189              208       224                            257                                                                             342-TPO                                                          408                                                  
                                                                                                                                                                                             345-TPO                                                                                                            
                                                                                                                                                                                              346-SEP
   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 5UIR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  IRAK4_HUMAN | Q9NWZ3
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  2.7.11.1
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 Related Entries

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UniProtKB/Swiss-Prot
        IRAK4_HUMAN | Q9NWZ3: 2nru 2nry 2o8y 2oib 2oic 2oid 3mop 4rmz 4u97 4u9a 4xs2 4y73 4yo6 4yp8 4ztl 4ztm 4ztn 5kx7 5kx8 5t1s 5t1t 5uiq 5uis 5uit 5uiu

(-) Related Entries Specified in the PDB File

5uiq 5uis 5uit 5uiu