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(-) Description

Title :  CRYSTAL STRUCTURE OF IRAK4 KINASE DOMAIN WITH INHIBITOR
 
Authors :  C. A. Lesburg
Date :  13 Feb 15  (Deposition) - 20 May 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
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, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lim, M. D. Altman, J. Baker, J. D. Brubaker, H. Chen, Y. Chen, T. Fischmann, C. Gibeau, M. A. Kleinschek, E. Leccese, C. Lesburg, J. K. Maclean, L. Y. Moy, E. F. Mulrooney, J. Presland, L. Rakhilina, G. F. Smith, D. Steinhuebel, R. Yang
Discovery Of 5-Amino-N-(1H-Pyrazol-4-Yl)Pyrazolo[1, 5-A]Pyrimidine-3-Carboxamide Inhibitors Of Irak4.
Acs Med. Chem. Lett. V. 6 683 2015
PubMed-ID: 26101574  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00107

(-) Compounds

Molecule 1 - INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4
    ChainsA, B, C, D
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    FragmentKINASE DOMAIN
    GeneIRAK4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIRAK-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
1SEP4Mod. Amino AcidPHOSPHOSERINE
2TPO8Mod. Amino AcidPHOSPHOTHREONINE
3XPY4Ligand/Ion5-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-N-[1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL]PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
3XPY1Ligand/Ion5-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-N-[1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL]PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
3XPY1Ligand/Ion5-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-N-[1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL]PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
3XPY1Ligand/Ion5-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-N-[1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL]PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE
3XPY1Ligand/Ion5-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-N-[1-METHYL-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-4-YL]PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:192 , GLY A:193 , GLU A:194 , GLY A:195 , VAL A:200 , ALA A:211 , TYR A:262 , VAL A:263 , MET A:265 , GLY A:268 , ASP A:272 , ALA A:315 , ASN A:316 , LEU A:318 , ASP A:329 , HOH A:1185 , HOH A:1187binding site for residue XPY A 1000
2AC2SOFTWAREMET B:192 , GLY B:193 , GLU B:194 , GLY B:195 , VAL B:200 , ALA B:211 , TYR B:262 , VAL B:263 , MET B:265 , GLY B:268 , ASP B:272 , ALA B:315 , ASN B:316 , LEU B:318 , ASP B:329 , HOH B:1174 , HOH B:1175binding site for residue XPY B 1000
3AC3SOFTWAREMET C:192 , GLY C:193 , GLU C:194 , VAL C:200 , ALA C:211 , VAL C:246 , TYR C:262 , VAL C:263 , TYR C:264 , MET C:265 , GLY C:268 , ALA C:315 , ASN C:316 , LEU C:318 , ASP C:329 , HOH C:1191binding site for residue XPY C 1000
4AC4SOFTWAREMET D:192 , GLY D:193 , GLU D:194 , GLY D:195 , VAL D:200 , ALA D:211 , LYS D:213 , TYR D:262 , VAL D:263 , MET D:265 , GLY D:268 , ASP D:272 , ALA D:315 , ASN D:316 , LEU D:318 , ASP D:329 , HOH D:1192 , HOH D:1198binding site for residue XPY D 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y73)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ala A:217 -Met A:218
2Asp A:220 -Ile A:221
3Glu A:392 -Pro A:393
4Ala B:217 -Met B:218
5Asp B:220 -Ile B:221
6Glu B:392 -Pro B:393
7Ala C:217 -Met C:218
8Asp C:220 -Ile C:221
9Glu C:392 -Pro C:393
10Ala D:217 -Met D:218
11Asp D:220 -Ile D:221
12Glu D:392 -Pro D:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y73)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y73)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhh......hhhhh..eeee...eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee......hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y73 A 163 TRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   ||  347       357       367       377       387       397       407       417       427       437       447       457  
                                                                                                                                                                                                       336|  ||                                                                                                                 
                                                                                                                                                                                                        342-TPO                                                                                                                 
                                                                                                                                                                                                           345-TPO                                                                                                              
                                                                                                                                                                                                            346-SEP                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhh.............eeee...eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeee.....eeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee........ee......hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y73 B 161 SDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   ||  347       357       367       377       387       397       407       417       427       437       447       457  
                                                                                                                                                                                                       334|  ||                                                                                                                 
                                                                                                                                                                                                        342-TPO                                                                                                                 
                                                                                                                                                                                                           345-TPO                                                                                                              
                                                                                                                                                                                                            346-SEP                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh......hhhhh..eeee...eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeee.....eeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...ee......hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y73 C 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS 460
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   ||  347       357       367       377       387       397       407       417       427       437       447       457   
                                                                                                                                                                                                       337|  ||                                                                                                                  
                                                                                                                                                                                                        342-TPO                                                                                                                  
                                                                                                                                                                                                           345-TPO                                                                                                               
                                                                                                                                                                                                            346-SEP                                                                                                              

Chain D from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhh......hhhhh..eeee...eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee......hhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y73 D 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  ||  |348       358       368       378       388       398       408       418       428       438       448       458 
                                                                                                                                                                                                      336|  ||                                                                                                                 
                                                                                                                                                                                                       342-TPO                                                                                                                 
                                                                                                                                                                                                          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 4Y73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y73)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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    Glu A:392 - Pro A:393   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        IRAK4_HUMAN | Q9NWZ32nru 2nry 2o8y 2oib 2oic 2oid 3mop 4rmz 4u97 4u9a 4xs2 4yo6 4yp8 4ztl 4ztm 4ztn 5kx7 5kx8 5t1s 5t1t 5uiq 5uir 5uis 5uit 5uiu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Y73)