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(-) Description

Title :  PAK1 IN COMPLEX WITH (S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
 
Authors :  S. Gutmann, G. Rummel
Date :  29 Apr 15  (Deposition) - 24 Jun 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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 :  Pak1, Inhibitor, Kinase, Allosteric, Transferase (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, C, D
    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
    Synonym: ALPHA-PAK,P21-ACTIVATED KINASE 1,PAK-1,P65-PAK

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
14OR4Ligand/Ion(S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14OR1Ligand/Ion(S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14OR1Ligand/Ion(S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
14OR1Ligand/Ion(S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
14OR1Ligand/Ion(S)-N-(TERT-BUTYL)-3-((2-CHLORO-5-ETHYL-8-FLUORO-DIBENZODIAZEPIN-11-YL)AMINO)PYRROLIDINE-1-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:301 , GLU 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 , HOH A:705 , HOH A:757 , HOH A:774 , HOH A:817binding site for residue 4OR A 601
2AC2SOFTWAREMET B:301 , GLU B:315 , MET B:319 , ASN B:322 , ILE B:327 , VAL B:328 , VAL B:342 , PHE B:379 , ASN B:383 , HIS B:387 , LEU B:405 , THR B:406 , HOH B:723 , HOH B:724 , HOH B:754binding site for residue 4OR B 601
3AC3SOFTWAREGLU C:315 , VAL C:318 , MET C:319 , ASN C:322 , ILE C:327 , VAL C:328 , VAL C:342 , PHE C:379 , LEU C:380 , ASN C:383 , HIS C:387 , LEU C:405 , THR C:406binding site for residue 4OR C 601
4AC4SOFTWAREGLU C:461 , HOH C:704 , HOH C:795 , HOH C:826binding site for residue MG C 602
5AC5SOFTWAREMET D:301 , GLU D:315 , VAL D:318 , MET D:319 , ASN D:322 , ILE D:327 , VAL D:328 , PHE D:379 , ASN D:383 , HIS D:387 , LEU D:405 , THR D:406 , ASP D:407 , PHE D:410 , HOH D:803binding site for residue 4OR D 601
6AC6SOFTWAREGLU D:461 , HOH D:701 , HOH D:709 , HOH D:747binding site for residue MG D 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZJJ)

(-) 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 hhhhhhhhhhhhh...hhhhheeeeeeeee....eeeeeee.....eeeeeee....hhhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.......ee.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zjj A 249 SDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKE 539
                                   258       268       278       288       298     ||312       322       332       342       352       362       372       382       392       402       412  ||   429       439       449       459       469       479       489       499       509       519       529       539
                                                                                 304|                                                                                                       415|                                                                                                                    
                                                                                  309                                                                                                        423                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...hhhhheeeeeeeeee..eeeeeeee.....eeeeeee...hhhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.......ee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhh...hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zjj B 251 EEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKE 539
                                   260       270       280       290       300  ||   315       325       335       345       355       365       375       385       395       405       415|      432       442       452       462       472       482       492       502       512       522       532       
                                                                              303|                                                                                                       415|                                                                                                                    
                                                                               309                                                                                                        423                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh...hhhhhheeeeeeee....eeeeee....eeeeeee....hhhhhhhhhhhhhh.......eeeee...eeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....hhhhhh.........hhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zjj C 251 EEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVAQEVAIKQMNLQKKELIINEILVMRENKNPNIVNYLDSYLVELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGEQSKRSTMVGTPYWMAPEVVTAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   260       270       280       290||     302 ||    315       325       335||     347       357       367       377       387       397       407 ||    424       434  ||   446       456       466       476       486       496       506       516       526       536      
                                                                  291|       304|                         336|                                                                   409|                 437|                                                                                                      
                                                                   294        308                          339                                                                    417                  440                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......eeeeeeee....eeeeee...eeeeee...hhhhhhhhhhhhhhh.......eeeee...eeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.......................hhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zjj D 252 EILEKLRSIVSVKKKYTRFEKIGQGASGTVYTAMDVEVAIKQMNLPKKELIINEILVMRENKNPNIVNYLDSYGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEAT 541
                                   261 ||    274       284     ||298    || 311       321       331  ||   343       353       363       373       383       393       403       417       427       437       447       457       467       477       487       497       507       517       527       537    
                                     263|                    290|     303|                        334|                                                                       411|                                                                                                                             
                                      267                     295      307                         337                                                                        416
   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 4ZJJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 61)

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

(-) Related Entries Specified in the PDB File

4zji