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(-) Description

Title :  IRAK4-INHIBITOR CO-STRUCTURE
 
Authors :  T. O. Fischmann
Date :  14 May 15  (Deposition) - 02 Sep 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
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. M. Seganish, T. O. Fischmann, B. Sherborne, J. Matasi, B. Lavey, W. T. Mcelroy, D. Tulshian, J. Tata, C. Sondey, C. G. Garlisi, K. Devito J. Fossetta, D. Lundell, X. Niu
Discovery And Structure Enabled Synthesis Of 2, 6-Diaminopyrimidin-4-One Irak4 Inhibitors.
Acs Med. Chem. Lett. V. 6 942 2015
PubMed-ID: 26288698  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00279

(-) 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 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
14S24Ligand/Ion5-(1,3-BENZOTHIAZOL-2-YL)-2-(CYCLOPROPYLAMINO)-6-{[(1R,2S,3R,4R)-2,3-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOPENTYL]AMINO}PYRIMIDIN-4(3H)-ONE
2SEP4Mod. Amino AcidPHOSPHOSERINE
3TPO8Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
14S21Ligand/Ion5-(1,3-BENZOTHIAZOL-2-YL)-2-(CYCLOPROPYLAMINO)-6-{[(1R,2S,3R,4R)-2,3-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOPENTYL]AMINO}PYRIMIDIN-4(3H)-ONE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
14S21Ligand/Ion5-(1,3-BENZOTHIAZOL-2-YL)-2-(CYCLOPROPYLAMINO)-6-{[(1R,2S,3R,4R)-2,3-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOPENTYL]AMINO}PYRIMIDIN-4(3H)-ONE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
14S21Ligand/Ion5-(1,3-BENZOTHIAZOL-2-YL)-2-(CYCLOPROPYLAMINO)-6-{[(1R,2S,3R,4R)-2,3-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOPENTYL]AMINO}PYRIMIDIN-4(3H)-ONE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
14S21Ligand/Ion5-(1,3-BENZOTHIAZOL-2-YL)-2-(CYCLOPROPYLAMINO)-6-{[(1R,2S,3R,4R)-2,3-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOPENTYL]AMINO}PYRIMIDIN-4(3H)-ONE
2SEP1Mod. Amino AcidPHOSPHOSERINE
3TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:192 , GLU A:194 , VAL A:200 , ALA A:211 , LYS A:213 , VAL A:246 , TYR A:262 , TYR A:264 , MET A:265 , PRO A:266 , GLY A:268 , ASP A:272 , ALA A:315 , LEU A:318 , SER A:328binding site for residue 4S2 A 501
2AC2SOFTWAREMET B:192 , ALA B:211 , LYS B:213 , VAL B:246 , TYR B:262 , TYR B:264 , MET B:265 , PRO B:266 , GLY B:268 , ASP B:272 , ALA B:315 , LEU B:318binding site for residue 4S2 B 501
3AC3SOFTWAREMET C:192 , VAL C:200 , ALA C:211 , LYS C:213 , VAL C:246 , TYR C:262 , TYR C:264 , MET C:265 , PRO C:266 , GLY C:268 , LEU C:318binding site for residue 4S2 C 501
4AC4SOFTWAREMET D:192 , GLU D:194 , ALA D:211 , VAL D:246 , TYR D:262 , 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:329binding site for residue 4S2 D 501

(-) SS Bonds  (0, 0)

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

(-) 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 4ZTM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZTM)

(-) 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhh.............eeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee....ee...........hhhhhh.ee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztm A 162 DTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLATTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEQtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   171       181       191       201       211    || 226       236       246       256       266       276       286       296       306       316       326       336|||  ||349       359       369       379       389       399       409       419       429       439       449       459
                                                                                216|                                                                                                                337||  ||                                                                                                                 
                                                                                 222                                                                                                                 341|  ||                                                                                                                 
                                                                                                                                                                                                      342-TPO                                                                                                                 
                                                                                                                                                                                                         345-TPO                                                                                                              
                                                                                                                                                                                                          346-SEP                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhh.............eee.....eeeeeee..eeeeeee..hhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee.........ee...........hhhhhh.ee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztm B 161 SDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLLKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARQtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   170       180       190       200       210    || 230       240       250       260       270       280       290       300       310       320       330   ||| 346       356       366       376       386       396       406       416       426       436       446       456   
                                                                                215|                                                                                                         334||  ||                                                                                                                 
                                                                                 226                                                                                                          341|  ||                                                                                                                 
                                                                                                                                                                                               342-TPO                                                                                                                 
                                                                                                                                                                                                  345-TPO                                                                                                              
                                                                                                                                                                                                   346-SEP                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhh............eeee....eeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeee...eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee...ee...........hhhhhh.ee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztm C 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEtVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS 460
                                   173       183       193       203       213 ||    228       238       248     ||261       271       281       291       301       311       321       331     ||345|      355       365       375       385       395       405       415       425       435       445       455     
                                                                             215|                              254|                                                                            337|  ||                                                                                                                  
                                                                              221                               258                                                                             342-TPO                                                                                                                  
                                                                                                                                                                                                   345-TPO                                                                                                               
                                                                                                                                                                                                    346-SEP                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhh......hhhhh..eeee..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee...........hhhhhh.ee.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhh........hhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztm D 164 RFHSFSFYELKNVTNNFDERPISVGGNKMGEGFGVVYKGYVNNTTVAVKKLATTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARAStVMtsRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA 459
                                   173       183       193 ||    204       214 ||    229       239       249       259       269       279       289       299       309       319       329      |344||     354       364       374       384       394       404       414       424       434       444       454     
                                                         195|                216|                                                                                                               336|  ||                                                                                                                 
                                                          197                 222                                                                                                                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 4ZTM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4ztm
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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 4ztn 5kx7 5kx8 5t1s 5t1t 5uiq 5uir 5uis 5uit 5uiu

(-) Related Entries Specified in the PDB File

4ztl 4ztn