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(-) Description

Title :  IRAK4-INHIBITOR CO-STRUCTURE
 
Authors :  T. O. Fischmann
Date :  21 Jan 15  (Deposition) - 13 May 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
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 :  Kinase, Phosphatase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. T. Mcelroy, W. Michael Seganish, R. Jason Herr, J. Harding, J. Yang, L. Yet, V. Komanduri, K. C. Prakash, B. Lavey, D. Tulshian, W. J. Greenlee, C. Sondey, T. O. Fischmann, X. Niu
Discovery And Hit-To-Lead Optimization Of 2, 6-Diaminopyrimidine Inhibitors Of Interleukin-1 Receptor-Associated Kinase 4.
Bioorg. Med. Chem. Lett. V. 25 1836 2015
PubMed-ID: 25870132  |  Reference-DOI: 10.1016/J.BMCL.2015.03.043

(-) 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 Common: FALL ARMYWORM
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 160-460
    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
142P4Ligand/Ion(1R,2S,3R,5R)-3-({5-(1,3-BENZOTHIAZOL-2-YL)-6-CHLORO-2-[(3-METHOXYPROPYL)AMINO]PYRIMIDIN-4-YL}AMINO)-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2-DIOL
2SEP4Mod. Amino AcidPHOSPHOSERINE
3TPO8Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
142P1Ligand/Ion(1R,2S,3R,5R)-3-({5-(1,3-BENZOTHIAZOL-2-YL)-6-CHLORO-2-[(3-METHOXYPROPYL)AMINO]PYRIMIDIN-4-YL}AMINO)-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2-DIOL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
142P1Ligand/Ion(1R,2S,3R,5R)-3-({5-(1,3-BENZOTHIAZOL-2-YL)-6-CHLORO-2-[(3-METHOXYPROPYL)AMINO]PYRIMIDIN-4-YL}AMINO)-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2-DIOL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
142P1Ligand/Ion(1R,2S,3R,5R)-3-({5-(1,3-BENZOTHIAZOL-2-YL)-6-CHLORO-2-[(3-METHOXYPROPYL)AMINO]PYRIMIDIN-4-YL}AMINO)-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2-DIOL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
142P1Ligand/Ion(1R,2S,3R,5R)-3-({5-(1,3-BENZOTHIAZOL-2-YL)-6-CHLORO-2-[(3-METHOXYPROPYL)AMINO]PYRIMIDIN-4-YL}AMINO)-5-(HYDROXYMETHYL)CYCLOPENTANE-1,2-DIOL
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:211 , LYS A:213 , TYR A:262 , VAL A:263 , TYR A:264 , MET A:265 , PRO A:266 , GLY A:268 , SER A:269 , ASP A:272 , ALA A:315 , LEU A:318 , ASP A:329binding site for residue 42P A 501
2AC2SOFTWAREMET B:192 , ALA B:211 , LYS B:213 , TYR B:262 , VAL B:263 , TYR B:264 , MET B:265 , PRO B:266 , GLY B:268 , SER B:269 , ASP B:272 , ALA B:315 , LEU B:318 , ASP B:329binding site for residue 42P B 501
3AC3SOFTWAREILE C:185 , MET C:192 , GLY C:193 , VAL C:200 , ALA C:211 , LYS C:213 , TYR C:262 , VAL C:263 , MET C:265 , PRO C:266 , GLY C:268 , SER C:269 , ASP C:272 , ALA C:315 , ASN C:316 , LEU C:318 , ASP C:329 , HOH C:604 , HOH C:609binding site for residue 42P C 501
4AC4SOFTWAREMET D:192 , GLY D:193 , GLU D:194 , ALA D:211 , LYS D:213 , TYR D:262 , VAL D:263 , TYR D:264 , MET D:265 , PRO D:266 , GLY D:268 , SER D:269 , ASP D:272 , ALA D:315 , LEU D:318 , ASP D:329 , HOH D:611binding site for residue 42P D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XS2)

(-) 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 4XS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XS2)

(-) Exons   (0, 0)

(no "Exon" information available for 4XS2)

(-) 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:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhh...........eee.....eeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...ee...........hhhhhhheehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs2 A 163 TRFHSFSFYELKNVTNNFDERPISVNKMGEGGFGVVYKGYVNNTTVAVKKLATTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   172       182    || 194       204       214 ||    229       239       249       259       269       279       289       299       309       319       329       343 ||    353       363       373       383       393       403       413       423       433       443       453      
                                                  187|                       216|                                                                                                                337|  ||                                                                                                                 
                                                   190                        222                                                                                                                 342-TPO                                                                                                                 
                                                                                                                                                                                                     345-TPO                                                                                                              
                                                                                                                                                                                                      346-SEP                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhh...........eeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee........ee...........hhhhhhheehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs2 B 161 SDTRFHSFSFYELKNVTNNFDERPISVNKMGEGGFGVVYKGYVNNTTVAVKKLALKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   170       180      |192       202       212   ||  231       241       251       261       271       281       291       301       311       321       331  ||  |348       358       368       378       388       398       408       418       428       438       448       458 
                                                    187|                       216|                                                                                                         334|  ||                                                                                                                 
                                                     190                        226                                                                                                          342-TPO                                                                                                                 
                                                                                                                                                                                                345-TPO                                                                                                              
                                                                                                                                                                                                 346-SEP                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhh........hhhhh..eeee....eeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeee..eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...ee...........hhhhhhheehhhhhhhhhhhhhhhhhhh............hhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs2 C 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLITTEELKQQFDQEIKVMAKCQHENLVELLGFSSLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS 460
                                   173       183       193       203       213 ||    228       238       248    || 262       272       282       292       302       312       322       332    || 346       356       366       376       386       396       406       416       426       436       446       456    
                                                                             215|                             253|                                                                            337|  ||                                                                                                                  
                                                                              221                              258                                                                             342-TPO                                                                                                                  
                                                                                                                                                                                                  345-TPO                                                                                                               
                                                                                                                                                                                                   346-SEP                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhh...........eee...eeeeeee..eeeeeee....hhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee...........hhhhhhheehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs2 D 164 RFHSFSFYELKNVTNNFDERPIGNKMGEGGVVYKGYVNNTTVAVKKLAAEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   173       183 ||    198       208       224       234       244       254       264       274       284       294       304       314       324       334 ||  ||349       359       369       379       389       399       409       419       429       439       449       459
                                               185|   195|                217|                                                                                                             336|  ||                                                                                                                 
                                                189    198                 224                                                                                                              342-TPO                                                                                                                 
                                                                                                                                                                                               345-TPO                                                                                                              
                                                                                                                                                                                                346-SEP
   Legend:   → Mismatch (orange background)
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  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 4XS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XS2)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4xs2
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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 4y73 4yo6 4yp8 4ztl 4ztm 4ztn 5kx7 5kx8 5t1s 5t1t 5uiq 5uir 5uis 5uit 5uiu

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