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(-) Description

Title :  CRYSTAL STRUCTURE OF IRAK4 IN COMPLEX WITH COMPOUND 12
 
Authors :  S. Han, J. S. Chang
Date :  14 Jan 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
18C14Ligand/Ion4-{[(3R)-PIPERIDIN-3-YL]OXY}-6-[(PROPAN-2-YL)OXY]QUINOLINE-7-CARBOXAMIDE
2TPO4Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
18C11Ligand/Ion4-{[(3R)-PIPERIDIN-3-YL]OXY}-6-[(PROPAN-2-YL)OXY]QUINOLINE-7-CARBOXAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
18C11Ligand/Ion4-{[(3R)-PIPERIDIN-3-YL]OXY}-6-[(PROPAN-2-YL)OXY]QUINOLINE-7-CARBOXAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
18C11Ligand/Ion4-{[(3R)-PIPERIDIN-3-YL]OXY}-6-[(PROPAN-2-YL)OXY]QUINOLINE-7-CARBOXAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
18C11Ligand/Ion4-{[(3R)-PIPERIDIN-3-YL]OXY}-6-[(PROPAN-2-YL)OXY]QUINOLINE-7-CARBOXAMIDE
2TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:194 , VAL A:200 , ALA A:211 , VAL A:263 , TYR A:264 , MET A:265 , GLY A:268 , ALA A:315 , ASN A:316 , LEU A:318 , HOH A:902binding site for residue 8C1 A 800
2AC2SOFTWAREGLU B:194 , ALA B:211 , VAL B:263 , TYR B:264 , MET B:265 , GLY B:268 , ALA B:315 , ASN B:316 , LEU B:318 , HOH B:912binding site for residue 8C1 B 801
3AC3SOFTWAREGLU C:194 , ALA C:211 , TYR C:262 , VAL C:263 , TYR C:264 , MET C:265 , GLY C:268 , ALA C:315 , ASN C:316 , LEU C:318 , HOH C:618binding site for residue 8C1 C 501
4AC4SOFTWAREMET D:192 , GLU D:194 , ALA D:211 , VAL D:263 , TYR D:264 , MET D:265 , GLY D:268 , ALA D:315 , LEU D:318 , HOH D:619binding site for residue 8C1 D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:392 -Pro A:393
2Gly B:195 -Gly B:196
3Gly B:196 -Phe B:197
4Glu B:392 -Pro B:393
5Glu C:392 -Pro C:393
6Glu D:392 -Pro D:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UIS)

(-) 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:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.hhhhhhhhh......hhhhh..eee...eeeeeee..eeeeeee..hhhhhhhhhhhhh.......eeeeeee..eeeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee....................hhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uis A 165 FHSFSFYELKNVTNNFDERPISVGGNKMGEGGVVYKGYVNNTTVAVKKLKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAMtSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174       184       194||     206       227       237       247       257       267       277       287       297       307       317       327       345       355       365       375       385       395       405|      418       428       438       448       458
                                                        195|              215|                                                                                                         335||                                                         405|                                                 
                                                         198               227                                                                                                          344|                                                          409                                                 
                                                                                                                                                                                         345-TPO                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhh........hhhhh..eeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.......eeeee..eeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee.............hhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uis B 165 FHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAEELKQQFDQEIKVMAKCQHENLVELLGFSSDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASMtSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174       184       194       204       214 ||    231       241       251 ||    264       274       284       294       304       314       324       334 |||   351       361       371       381       391       401   ||  413       423       433       443       453     
                                                                             216|                          253|                                                                            336||                                                         405|                                                  
                                                                              224                           257                                                                             344|                                                          408                                                  
                                                                                                                                                                                             345-TPO                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhh......hhhhh..eee...eeeeeee..eeeeeee...hhhhhhhhhhhhhhh.......eeee..eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee....................hhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uis C 162 DTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGVVYKGYVNNTTVAVKKLAELKQQFDQEIKVMAKCQHENLVELLGFSLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAMtSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   171       181       191   ||  203       213  ||   231       241       251||     266       276       286       296       306       316       326       344|      354       364       374       384       394       404||     417       427       437       447       457 
                                                           195|               216|                        252|                                                                          335||                                                         405|                                                 
                                                            198                225                         258                                                                           344|                                                          409                                                 
                                                                                                                                                                                          345-TPO                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhh...........eeeee...eeeee..hhhhhhhhhh.......eeee..eeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee....................hhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uis D 165 FHSFSFYELKNVTNDERPKMGEGGVVYKGYVTVAVKKLFDQEIKVMAKCQHENLVELLGFSCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAMtSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT 458
                                   174   ||  192  ||   204||     231       241       251||     267       277       287       297       307       317       327       345       355       365       375       385       395       405|      417       427       437       447       457 
                                       178|  || 195|    205|   215|                   252|                                                                         335||                                                         405|                                                  
                                        181  ||  198     209    230                    259                                                                          344|                                                          408                                                  
                                           184|                                                                                                                      345-TPO                                                                                                           
                                            191
   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 5UIS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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  5uis
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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 5uiq 5uir 5uit 5uiu

(-) Related Entries Specified in the PDB File

5uiq 5uir 5uit 5uiu