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(-) Description

Title :  CRYSTAL STRUCTURE OF PAK1 IN COMPLEX WITH AN INHIBITOR COMPOUND 5
 
Authors :  A. Oh, C. Tam, W. Wang
Date :  26 Aug 15  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. O. Ndubaku
Design Of Selective Pak1 Inhibitor G-5555: Improving Proper-Ties By Employing An Unorthodox Low-Pka Polar Moiety
To Be Published
PubMed: search

(-) 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
    Fragment: PROTEIN KINASE DOMAIN RESIDUE 249-545
    Gene: PAK1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-PAK,P21-ACTIVATED KINASE 1,PAK-1,P65-PAK

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
159N2Ligand/Ion8-[(TRANS-4-AMINOCYCLOHEXYL)METHYL]-6-[2-CHLORO-4-(6-METHYLPYRAZIN-2-YL)PHENYL]-2-(ETHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
159N1Ligand/Ion8-[(TRANS-4-AMINOCYCLOHEXYL)METHYL]-6-[2-CHLORO-4-(6-METHYLPYRAZIN-2-YL)PHENYL]-2-(ETHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
159N1Ligand/Ion8-[(TRANS-4-AMINOCYCLOHEXYL)METHYL]-6-[2-CHLORO-4-(6-METHYLPYRAZIN-2-YL)PHENYL]-2-(ETHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:299 , GLU A:315 , MET A:344 , GLU A:345 , TYR A:346 , LEU A:347 , ASP A:393 , LEU A:396 , THR A:406 , HOH A:712 , HOH A:743 , HOH A:832binding site for residue 59N A 601
2AC2SOFTWAREALA B:297 , LYS B:299 , MET B:301 , MET B:319 , MET B:344 , GLU B:345 , TYR B:346 , LEU B:347 , ASP B:393 , ASN B:394 , LEU B:396 , THR B:406 , HOH B:753 , HOH B:839binding site for residue 59N B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DEW)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln B:304 -Gln B:305
2Gly B:480 -Thr B:481
3Asn B:486 -Pro B:487

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DEW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DEW)

(-) Exons   (0, 0)

(no "Exon" information available for 5DEW)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....hhhh.eeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dew A 250 DEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNN 544
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539     


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhheeeeeeee.....eeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh.......eeeeeee..eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dew B 255 EKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404     ||421       431       441       451       461       471       481       491       501       511       521       531       541 
                                                                                                                                                                                     410|                                                                                                                            
                                                                                                                                                                                      418
   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 5DEW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DEW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DEW)

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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  PAK1_HUMAN | Q13153
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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 4zlo 4zy4 4zy5 4zy6 5dey 5dfp 5ime 5kbq 5kbr

(-) Related Entries Specified in the PDB File

5dey 5dfp