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(-) Description

Title :  PAK1 IN COMPLEX WITH 2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
 
Authors :  S. Gutmann, G. Rummel
Date :  29 Apr 15  (Deposition) - 24 Jun 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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 :  Inhibitor, Kinase, Pak1, 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
14OQ4Ligand/Ion2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14OQ1Ligand/Ion2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14OQ1Ligand/Ion2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
14OQ1Ligand/Ion2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
14OQ1Ligand/Ion2-CHLORO-5-ETHYL-8-FLUORO-11-(4-METHYLPIPERAZIN-1-YL)-DIBENZODIAZEPINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:315 , VAL A:318 , MET A:319 , ASN A:322 , ILE A:327 , VAL A:328 , PHE A:379 , LEU A:380 , ASN A:383 , HIS A:387 , LEU A:405 , THR A:406 , ASP A:407 , ALA A:412 , HOH A:724binding site for residue 4OQ A 601
2AC2SOFTWAREGLU B:315 , VAL B:318 , MET B:319 , ASN B:322 , ILE B:327 , VAL B:328 , PHE B:379 , LEU B:380 , ASN B:383 , HIS B:387 , LEU B:405 , THR B:406 , ASP B:407 , ALA B:412binding site for residue 4OQ B 601
3AC3SOFTWAREGLU C:315 , VAL C:318 , MET C:319 , ASN C:322 , ILE C:327 , VAL C:328 , LEU C:380 , ASN C:383 , HIS C:387 , LEU C:405 , THR C:406 , ASP C:407 , ALA C:412 , HOH C:754binding site for residue 4OQ C 601
4AC4SOFTWAREGLU C:461 , HOH C:701 , HOH C:725 , HOH C:778 , HOH C:779 , HOH C:807binding site for residue MG C 602
5AC5SOFTWAREGLU D:315 , VAL D:318 , ASN D:322 , ILE D:327 , VAL D:328 , ASN D:383 , HIS D:387 , LEU D:405 , THR D:406 , ASP D:407 , ALA D:412 , HOH D:734binding site for residue 4OQ D 601
6AC6SOFTWAREGLU D:461 , HOH D:701 , HOH D:735 , HOH D:764 , HOH D:768 , HOH D:806binding site for residue MG D 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZJI)

(-) 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 hhhhhhhh...hhhhheeeeeeeee....eeeeeee.....eeeeeeee..hhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.......ee......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zji A 254 LEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   263       273       283       293       303|      318       328       338       348       358       368       378       388       398       408       424       434       444       454       464       474       484       494       504       514       524       534        
                                                                           303|                                                                                                        416|                                                                                                                       
                                                                            309                                                                                                         423                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh...hhhhheeeeeeeee....eeeeeee.....eeeeeeee...hhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.......ee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zji B 254 LEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEA 540
                                   263       273       283       293       303||     318       328       338       348       358       368       378       388       398       408       424       434       444       454       464       474       484       494       504       514       524       534      
                                                                            304|                                                                                                       416|                                                                                                                     
                                                                             310                                                                                                        423                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhheeeeeeee....eeeeee.....eeeeeee..hhhhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....................hhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zji C 250 DEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDATGQEVAIKQMNKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEAT 541
                                   259       269       279       289|      300 ||    315       325       335       345       355       365       375       385       395       405       420       430       440       450       460       470       480       490       500       510       520       530       540 
                                                                 289|        302|                                                                                                      413|                                                                                                                          
                                                                  291         308                                                                                                       419                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhheeeeeeeeee..eeeeeeee.....eeeeeee..hhhhhhhhhhhhhh.......eeeeeee..eeeeee.....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......................hhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhh.hhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zji D 253 ILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFAQITSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEAT 541
                                   262       272       282       292       302|      317       327       337       347       357       367       377       387       397       407  ||  |421       431       441       451       461       471       481       491       501       511       521       531       541
                                                                           302|                                                                                                   410|  ||                                                                                                                          
                                                                            308                                                                                                    412  ||                                                                                                                          
                                                                                                                                                                                      415|                                                                                                                          
                                                                                                                                                                                       419
   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 4ZJI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 61)

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

(-) Related Entries Specified in the PDB File

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