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(-) Description

Title :  SERINE/THREONINE-PROTEIN KINASE PAK1 COMPLEXED WITH A DIBENZODIAZEPINE: IDENTIFICATION OF AN ALLOSTERIC SITE ON PAK1
 
Authors :  C. R. Bellamacina, D. E. Bussiere
Date :  01 May 15  (Deposition) - 05 Aug 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Dibenzodazepine, Pak1, Kinase, Allosteric Inhibitor, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Karpov, P. Amiri, C. Bellamacina, M. H. Bellance, W. Breitenstein, D. Daniel, R. Denay, D. Fabbro, C. Fernandez, I. Galuba, S. Guerro-Lagasse, S. Gutmann, L. Hinh, W. Jahnke, J. Klopp A. Lai, M. K. Lindvall, S. Ma, H. Mobitz, S. Pecchi, G. Rummel, K. Shoemaker, J. Trappe, C. Voliva, S. W. Cowan-Jacob, A. L. Marzinzik
Optimization Of A Dibenzodiazepine Hit To A Potent And Selective Allosteric Pak1 Inhibitor.
Acs Med. Chem. Lett. V. 6 776 2015
PubMed-ID: 26191365  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00102

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PAK 1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PAK1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RESIDUE 177 IS PHOSPHORYLATED THREONINE
    Synonym: ALPHA-PAK,P21-ACTIVATED KINASE 1,PAK-1,P65-PAK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
14PV1Ligand/Ion2,8-DIFLUORO-11-(4-METHYLPIPERAZIN-1-YL)-5H-DIBENZO[B,E][1,4]DIAZEPINE
2GOL1Ligand/IonGLYCEROL
3TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
14PV1Ligand/Ion2,8-DIFLUORO-11-(4-METHYLPIPERAZIN-1-YL)-5H-DIBENZO[B,E][1,4]DIAZEPINE
2GOL1Ligand/IonGLYCEROL
3TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
14PV1Ligand/Ion2,8-DIFLUORO-11-(4-METHYLPIPERAZIN-1-YL)-5H-DIBENZO[B,E][1,4]DIAZEPINE
2GOL1Ligand/IonGLYCEROL
3TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:315 , VAL A:318 , MET A:319 , ASN A:322 , ILE A:327 , VAL A:328 , ASN A:383 , HIS A:387 , LEU A:405 , THR A:406 , GOL A:602binding site for residue 4PV A 601
2AC2SOFTWAREMET A:319 , VAL A:328 , MET A:344 , THR A:406 , ASP A:407 , PHE A:408 , 4PV A:601binding site for residue GOL A 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZLO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZLO)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhheeeeeeee...eeeeeee.....eeeeeee..hhhhhhhhhhhhhh.......eeeeeee..eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zlo A 250 DEEILEKLRSIVSVGDPKKKYTRFEKIGQSGTVYTAMDVATGQEVAIKQMNKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGSKRStMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKN 543
                                   259       269       281       291       301||     316       326       336       346       356       366       376       386       396       406  ||   425       435       445       455       465       475       485       495       505       515       525       535        
                                                      278|                  302|                                                                                                  409|   |                                                                                                                        
                                                       281                   308                                                                                                   419   |                                                                                                                        
                                                                                                                                                                                       423-TPO                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....eee....eee....hhhhhhhhhhhh.......eee...eee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zlo B 253 ILEKLRSIVSVKKKYTRFEKIGQVYTAMGQEVAIKQMELIINEILVMRENKNPNIVNYLDSYVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRStMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKN 543
                                   262||     275  ||   294      |312       322       332 ||    349       359       369       379       389       399       409       419   |   429       439       449       459       469       479       489       499       509       519       529       539    
                                    263|        278| 288|     301|                     334|                                                                              423-TPO                                                                                                                    
                                     267         284  293      310                      342
   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 4ZLO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 61)

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  PAK1_HUMAN | Q13153
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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
        PAK1_HUMAN | Q13153: 1f3m 1yhv 1yhw 1zsg 2hy8 2qme 3dvp 3fxz 3fy0 3q4z 3q52 3q53 4daw 4eqc 4o0r 4o0t 4p90 4zji 4zjj 4zy4 4zy5 4zy6 5dew 5dey 5dfp 5ime 5kbq 5kbr

(-) Related Entries Specified in the PDB File

4zji 4ZJJ CONTAINS THE SAME PROTEIN COMPLEXED WITH AN ANALOG
4zjj 4ZJJ CONTAINS THE SAME PROTEIN COMPLEXED WITH AN ANALOG