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(-) Description

Title :  STRUCTURE OF ULK1 BOUND TO A POTENT INHIBITOR
 
Authors :  M. B. Lazarus, C. J. Novotny, K. M. Shokat
Date :  14 Oct 14  (Deposition) - 14 Jan 15  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
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, Autophagy, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Lazarus, C. J. Novotny, K. M. Shokat
Structure Of The Human Autophagy Initiating Kinase Ulk1 In Complex With Potent Inhibitors.
Acs Chem. Biol. V. 10 257 2015
PubMed-ID: 25551253  |  Reference-DOI: 10.1021/CB500835Z

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE ULK1
    ChainsA, B, C, D
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-283
    GeneULK1, KIAA0722
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAUTOPHAGY-RELATED PROTEIN 1 HOMOLOG,HATG1,UNC-51-LIKE KINASE 1

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
13RJ4Ligand/IonN~2~-(1H-BENZIMIDAZOL-6-YL)-N~4~-(5-CYCLOBUTYL-1H-PYRAZOL-3-YL)QUINAZOLINE-2,4-DIAMINE
2GOL2Ligand/IonGLYCEROL
3TPO4Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
13RJ1Ligand/IonN~2~-(1H-BENZIMIDAZOL-6-YL)-N~4~-(5-CYCLOBUTYL-1H-PYRAZOL-3-YL)QUINAZOLINE-2,4-DIAMINE
2GOL2Ligand/IonGLYCEROL
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
13RJ1Ligand/IonN~2~-(1H-BENZIMIDAZOL-6-YL)-N~4~-(5-CYCLOBUTYL-1H-PYRAZOL-3-YL)QUINAZOLINE-2,4-DIAMINE
2GOL-1Ligand/IonGLYCEROL
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
13RJ1Ligand/IonN~2~-(1H-BENZIMIDAZOL-6-YL)-N~4~-(5-CYCLOBUTYL-1H-PYRAZOL-3-YL)QUINAZOLINE-2,4-DIAMINE
2GOL-1Ligand/IonGLYCEROL
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
13RJ1Ligand/IonN~2~-(1H-BENZIMIDAZOL-6-YL)-N~4~-(5-CYCLOBUTYL-1H-PYRAZOL-3-YL)QUINAZOLINE-2,4-DIAMINE
2GOL-1Ligand/IonGLYCEROL
3TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:130 , ILE A:134 , ILE A:135 , LEU A:172 , PHE A:269binding site for residue GOL A 301
2AC2SOFTWAREHIS A:130 , SER A:131 , GLY A:133 , LEU A:172 , HOH A:462 , SER B:131 , GLY B:133binding site for residue GOL A 302
3AC3SOFTWAREILE A:22 , ALA A:44 , GLU A:93 , TYR A:94 , CYS A:95 , ASN A:96 , GLY A:98 , ASP A:102 , GLN A:142 , ASN A:143 , LEU A:145 , HOH A:425 , HOH A:460binding site for residue 3RJ A 303
4AC4SOFTWAREILE B:22 , ALA B:44 , GLU B:93 , TYR B:94 , CYS B:95 , GLY B:98 , ASP B:99 , GLN B:142 , ASN B:143 , LEU B:145binding site for residue 3RJ B 401
5AC5SOFTWAREILE C:22 , ALA C:44 , GLU C:93 , TYR C:94 , CYS C:95 , ASN C:96 , GLY C:98 , ASP C:102 , GLN C:142 , ASN C:143 , LEU C:145binding site for residue 3RJ C 401
6AC6SOFTWAREILE D:22 , ALA D:44 , LYS D:46 , GLU D:93 , TYR D:94 , CYS D:95 , GLY D:98 , ASP D:99 , GLN D:142 , ASN D:143 , LEU D:145 , HOH D:539binding site for residue 3RJ D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp B:279 -Ala B:280
2Asp D:279 -Ala D:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WNP)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeeeeee....eeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee..hhhhhhhhhheeee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnp A   7 GTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAAtLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDA 280
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   |   186       196       206       216       226       236       246       256       266       276    
                                                                                                                                                                                                       180-TPO                                                                                                

Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeeeeeeeee..eeeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee.......hhhhheeee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnp B   8 TETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAAtLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDA 280
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  |    187       197       207       217       227       237       247       257       267       277   
                                                                                                                                                                                                      180-TPO                                                                                                

Chain C from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeeeeeeee....eeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee..hhhhhhhhhheeee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnp C   8 TETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAAtLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLD 279
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  |    187       197       207       217       227       237       247       257       267       277  
                                                                                                                                                                                                      180-TPO                                                                                               

Chain D from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeeeeeeee....eeeeeee......eeeeee.hhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee.......hhhhheeee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnp D   8 TETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAAtLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDA 280
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  |    187       197       207       217       227       237       247       257       267       277   
                                                                                                                                                                                                      180-TPO                                                                                                

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4WNP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        ULK1_HUMAN | O753854wno 5ci7

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4wno