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(-) Description

Title :  CRYSTAL STRUCTURE OF P21-ACTIVATED KINASE 1 (PAK1) IN COMPLEX WITH COMPOUND 9
 
Authors :  D. Li, W. Wang
Date :  06 Mar 16  (Deposition) - 25 May 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
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 :  J. Rudolph, L. J. Murray, C. O. Ndubaku, T. O'Brien, E. Blackwood, W. Wang, I. Aliagas, L. Gazzard, J. J. Crawford, J. Drobnick, W. Lee, X. Zhao, K. P. Hoeflich, D. A. Favor, P. Dong, H. Zhang, C. E. Heise, A. Oh C. C. Ong, H. La, P. Chakravarty, C. Chan, D. Jakubiak, J. Epler, S. Ramaswamy, R. Vega, G. Cain, D. Diaz, Y. Zhong
Chemically Diverse Group I P21-Activated Kinase (Pak) Inhibitors Impart Acute Cardiovascular Toxicity With A Narrow Therapeutic Window.
J. Med. Chem. V. 59 5520 2016
PubMed-ID: 27167326  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00638

(-) 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: RESIDUES 249-545
    Gene: PAK1
    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
16BZ2Ligand/Ion8-(3-AMINOPROPYL)-6-[2-CHLORO-4-(3-METHYL-2-OXOPYRAZIN-1(2H)-YL)PHENYL]-2-(METHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16BZ1Ligand/Ion8-(3-AMINOPROPYL)-6-[2-CHLORO-4-(3-METHYL-2-OXOPYRAZIN-1(2H)-YL)PHENYL]-2-(METHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16BZ1Ligand/Ion8-(3-AMINOPROPYL)-6-[2-CHLORO-4-(3-METHYL-2-OXOPYRAZIN-1(2H)-YL)PHENYL]-2-(METHYLAMINO)PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:297 , LYS A:299 , GLU A:315 , ILE A:316 , VAL A:342 , MET A:344 , GLU A:345 , TYR A:346 , LEU A:347 , LEU A:396 , THR A:406 , ASP A:407binding site for residue 6BZ A 601
2AC2SOFTWAREALA B:297 , LYS B:299 , VAL B:342 , MET B:344 , GLU B:345 , TYR B:346 , LEU B:347 , LEU B:396 , THR B:406 , ASP B:407 , HOH B:749binding site for residue 6BZ B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:278 -Gly A:279
2Ser A:281 -Gly A:282
3Gly B:279 -Ala B:280
4Ala B:280 -Ser B:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IME)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..............eeeee....eeeeee...hhhhhhhhhhhh........eeeee.....eeeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee.....eee......ee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ime A 251 EEILEKLRSIVSVGDPKKIGQGASGTVYTAMDQEVAIKQMNLKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNHG 546
                                   260      |277       287 ||    301 ||    316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546
                                          267|           289|      303|                                                                                                                                                                                                                                             
                                           275            294       309                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhheeeeeeee.....eeeeeee.....eeeeeee.......hhhhhhhhhh.......eeeeeee..eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ime B 250 DEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEAT 541
                                   259       269       279       289       299  ||   313       323       333       343       353       363       373       383       393       403    || 421       431       441       451       461       471       481       491       501       511       521       531       541
                                                                              302|                                                                                                  408|                                                                                                                            
                                                                               307                                                                                                   417
   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 5IME)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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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 4zlo 4zy4 4zy5 4zy6 5dew 5dey 5dfp 5kbq 5kbr

(-) Related Entries Specified in the PDB File

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