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(-) Description

Title :  BACK POCKET FLEXIBILITY PROVIDES GROUP-II PAK SELECTIVITY FOR TYPE 1 KINASE INHIBITORS
 
Authors :  A. Oh, C. Tam, W. Wang
Date :  14 Dec 13  (Deposition) - 12 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Pak1, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Staben, J. A. Feng, K. Lyle, M. Belvin, J. Boggs, J. D. Burch, C. C. Chua, H. Cui, A. G. Dipasquale, L. S. Friedman, C. Heise, H. Koeppen, A. Kotey, R. Mintzer, A. Oh, D. A. Roberts, L. Rouge, J. Rudolph, C. Tam, W. Wang, Y. Xiao, A. Young, Y. Zhang, K. P. Hoeflich
Back Pocket Flexibility Provides Group Ii P21-Activated Kinase (Pak) Selectivity For Type I 1/2 Kinase Inhibitors.
J. Med. Chem. V. 57 1033 2014
PubMed-ID: 24432870  |  Reference-DOI: 10.1021/JM401768T

(-) 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: UNP 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
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
12OL1Ligand/Ion1-({1-(2-AMINOPYRIMIDIN-4-YL)-2-[(2-METHOXYETHYL)AMINO]-1H-BENZIMIDAZOL-6-YL}ETHYNYL)CYCLOHEXANOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12OL1Ligand/Ion1-({1-(2-AMINOPYRIMIDIN-4-YL)-2-[(2-METHOXYETHYL)AMINO]-1H-BENZIMIDAZOL-6-YL}ETHYNYL)CYCLOHEXANOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
12OL-1Ligand/Ion1-({1-(2-AMINOPYRIMIDIN-4-YL)-2-[(2-METHOXYETHYL)AMINO]-1H-BENZIMIDAZOL-6-YL}ETHYNYL)CYCLOHEXANOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12OL1Ligand/Ion1-({1-(2-AMINOPYRIMIDIN-4-YL)-2-[(2-METHOXYETHYL)AMINO]-1H-BENZIMIDAZOL-6-YL}ETHYNYL)CYCLOHEXANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:276 , VAL A:284 , LYS A:299 , GLU A:315 , MET A:319 , VAL A:328 , MET A:344 , GLU A:345 , TYR A:346 , LEU A:347 , SER A:351 , THR A:406 , ASP A:407 , PHE A:408BINDING SITE FOR RESIDUE 2OL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O0T)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:265 -Pro A:266
2Ala A:291 -Thr A:292
3Thr A:292 -Gly A:293
4Lys A:308 -Lys A:309
5Gln B:304 -Gln B:305
6Glu B:417 -Gln B:418

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O0T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O0T)

(-) Exons   (0, 0)

(no "Exon" information available for 4O0T)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4o0ta_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..........eeeeeeeeee..eeeeeeee.....eeeeeeee......hhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o0t A 251 EEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540  


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4o0tb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhheeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o0t B 255 EKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404   ||  422       432       442       452       462       472       482       492       502       512       522       532       542
                                                                                                                                                                                   408|                                                                                                                             
                                                                                                                                                                                    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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O0T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O0T)

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Asp A:265 - Pro A:266   [ RasMol ]  
    Gln B:304 - Gln B:305   [ RasMol ]  
    Glu B:417 - Gln B:418   [ RasMol ]  
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  4o0t
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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 4p90 4zji 4zjj 4zlo 4zy4 4zy5 4zy6 5dew 5dey 5dfp 5ime 5kbq 5kbr

(-) Related Entries Specified in the PDB File

4o0r 4o0v 4o0x 4o0y