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(-) Description

Title :  CRYSTAL STRUCTURE OF IRAK4 IN COMPLEX WITH COMPOUND 9
 
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,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
18BV4Ligand/Ion2-[(PROPAN-2-YL)OXY]BENZAMIDE
2SEP4Mod. Amino AcidPHOSPHOSERINE
3TPO8Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
18BV1Ligand/Ion2-[(PROPAN-2-YL)OXY]BENZAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
18BV1Ligand/Ion2-[(PROPAN-2-YL)OXY]BENZAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
18BV1Ligand/Ion2-[(PROPAN-2-YL)OXY]BENZAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
18BV1Ligand/Ion2-[(PROPAN-2-YL)OXY]BENZAMIDE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:192 , ALA A:211 , TYR A:262 , VAL A:263 , TYR A:264 , MET A:265 , LEU A:318binding site for residue 8BV A 501
2AC2SOFTWAREALA B:211 , TYR B:262 , VAL B:263 , TYR B:264 , MET B:265 , LEU B:318binding site for residue 8BV B 501
3AC3SOFTWAREVAL C:200 , ALA C:211 , TYR C:262 , VAL C:263 , TYR C:264 , MET C:265 , LEU C:318 , SER C:328binding site for residue 8BV C 501
4AC4SOFTWAREALA D:211 , TYR D:262 , VAL D:263 , MET D:265 , LEU D:318binding site for residue 8BV D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:392 -Pro A:393
2Glu B:392 -Pro B:393
3Glu C:392 -Pro C:393
4Glu D:392 -Pro D:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UIQ)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh.........eee..eeeeee....eeeeee...hhhhhhhhhhhhh.......eeee....eeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee...ee...........hhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uiq A 164 RFHSFSFYELKNVTNNFDERPKMGEGGFGVVYKGYVTTVAVKKLAAKQQFDQEIKVMAKCQHENLVELLGFSSDCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASQtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   173       183||     199     ||211     ||230       240       250   ||  264       274       284       294       304       314       324       334 |||  |348       358       368       378       388       398       408       418       428       438       448       458 
                                              184|           205|      217|                        254|                                                                          336||  ||                                                                                                                 
                                               191            208       227                         259                                                                           341|  ||                                                                                                                 
                                                                                                                                                                                   342-TPO                                                                                                                 
                                                                                                                                                                                      345-TPO                                                                                                              
                                                                                                                                                                                       346-SEP                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh..........eee....eeeeee....eeeeee...hhhhhhhhhhhhhhhh.......eeeee....eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee..ee...........hhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uiq B 164 RFHSFSFYELKNVTNNFDERPIGNKMGEGGFGVVYKGYVTTVAVKKLAAEELKQQFDQEIKVMAKCQHENLVELLGFSSDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   173       183 ||    196       208       224       234       244       254|      266       276       286       296       306       316       326       336|  ||  351       361       371       381       391       401   ||  413       423       433       443       453     
                                               185|             205|      217|                           254|                                                                            336|  ||                                                        405|                                                  
                                                189              208       224                            257                                                                             342-TPO                                                         408                                                  
                                                                                                                                                                                             345-TPO                                                                                                           
                                                                                                                                                                                              346-SEP                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh......hhhhh..eee....eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee...eeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee...ee..................eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uiq C 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAATTEELKQQFDQEIKVMAKCQHENLVELLGFSSDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASQtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   173       183       193       203       213   ||  227       237       247      |259       269       279       289       299       309       319       329      |343 ||    353       363       373       383       393       403 ||    415       425       435       445       455   
                                                                               217|                             254|                                                                            336||  ||                                                        405|                                                  
                                                                                222                              257                                                                             341|  ||                                                         408                                                  
                                                                                                                                                                                                  342-TPO                                                                                                              
                                                                                                                                                                                                     345-TPO                                                                                                           
                                                                                                                                                                                                      346-SEP                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh......hhhhh.......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhh.......eeeee...eeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee.........ee..................eehhhhhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uiq D 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGGFGVVYKGYVNNTTVAVKKLALKQQFDQEIKVMAKCQHENLVELLGFSSDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   173       183       193|      205       215||     234       244       254|      266       276       286       296       306       316       326       342  ||   352       362       372       382       392       402  ||   414       424       434       444       454    
                                                       193|                 216|                         254|                                                                           335|  ||                                                        405|                                                  
                                                        196                  226                          257                                                                            342-TPO                                                         408                                                  
                                                                                                                                                                                            345-TPO                                                                                                           
                                                                                                                                                                                             346-SEP
   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 5UIQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  5uiq
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  IRAK4_HUMAN | Q9NWZ3
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  2.7.11.1
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 Related Entries

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

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 5uir 5uis 5uit 5uiu

(-) Related Entries Specified in the PDB File

5uir 5uis 5uit 5uiu