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(-) Description

Title :  RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH BENZIMIDAZOLE
 
Authors :  A. K. Charnley, M. A. Convery, A. Lakdawala Shah, E. Jones, P. Hardwick A. Bridges, B. J. Votta, P. J. Gough, R. W. Marquis, J. Bertin, L. Casill
Date :  24 Sep 15  (Deposition) - 21 Oct 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Kinase Domain, Kinase Inhibitor, Structure-Based Drug Design, Inhibitor Selectivity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Charnley, M. A. Convery, A. Lakdawala Shah, E. Jones, P. Hardwicke, A. Bridges, M. Ouellette, R. Totoritis, B. Schwartz, B. W. King, D. D. Wisnoski, J. Kang, P. M. Eidam, B. J. Votta, P. J. Gough, R. W. Marquis, J. Bertin, L. Casillas
Crystal Structures Of Human Rip2 Kinase Catalytic Domain Complexed With Atp-Competitive Inhibitors: Foundations For Understanding Inhibitor Selectivity.
Bioorg. Med. Chem. V. 23 7000 2015
PubMed-ID: 26455654  |  Reference-DOI: 10.1016/J.BMC.2015.09.038

(-) Compounds

Molecule 1 - RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2
    Chains: A, B
    EC Number: 2.7.10.2, 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN, UNP RESIDUES 1-310
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME- ASSOCIATED KINASE, CARD-CONTAINING IL-1 BETA ICE-KINASE, RIP-LIKE- INTERACTING CLARP KINASE, RECEPTOR-INTERACTING PROTEIN 2, RIP-2, TYROSINE-PROTEIN KINASE RIPK2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2IQ72Ligand/Ion2-(2-(4-CHLOROPHENYL)-1H-IMIDAZOL-5-YL)-N,1-BIS(2-METHOXYETHYL)-1H-BENZO[D]IMIDAZOLE-5-CARBOXAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:112 , HOH A:2072 , HOH A:2073 , HOH A:2074 , HOH A:2147BINDING SITE FOR RESIDUE CA A1311
2AC2SOFTWAREARG A:22 , TYR A:23 , LEU A:24 , SER A:25 , VAL A:32 , ALA A:45 , LYS A:47 , LEU A:79 , THR A:95 , GLU A:96 , TYR A:97 , MET A:98 , ASP A:164BINDING SITE FOR RESIDUE IQ7 A1312
3AC3SOFTWARETYR B:23 , LEU B:24 , SER B:25 , VAL B:32 , ALA B:45 , LYS B:47 , LEU B:79 , THR B:95 , GLU B:96 , TYR B:97 , MET B:98 , ASP B:164 , HOH B:2065BINDING SITE FOR RESIDUE IQ7 B1311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AR5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:139 -Pro A:140
2Thr B:139 -Pro B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AR5)

(-) Exons   (0, 0)

(no "Exon" information available for 5AR5)

(-) Sequences/Alignments

Asymmetric/Biological 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhh.eeeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee....hhh.eee.....eee......ee..........hhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ar5 A   4 EAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMEGGTIIYMPPENYEPSIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLEAVIQLK 310
                                    13        23        33        43      ||57        67        77        87        97       107       117       127       137       147       157       167    || 190       200|      216       226       236       246       256       266       276       286       296       306    
                                                                         50|                                                                                                                  172|           200|                                                                                                       
                                                                          55                                                                                                                   186            207                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhh.eeeeeeeee....eeeeeee.....eeeeee.....hhhhhhhhhhhhhhhh.......eeeeee....eeeeee.....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...ee....hhh.eee.....eee......ee......hhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhh................hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ar5 B   4 EAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRTIIYMPPENYESIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLEAVIQLK 310
                                    13        23        33        43      ||57        67        77        87        97       107       117       127       137       147       157       167   ||  194    || 211       221       231       241       251       261       271       281       291       301         
                                                                         50|                                                                                                                 171|       199|                                                                                                       
                                                                          55                                                                                                                  189        207
   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 5AR5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AR5)

(-) Gene Ontology  (74, 74)

Asymmetric/Biological Unit(hide GO term definitions)

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    Thr A:139 - Pro A:140   [ RasMol ]  
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  RIPK2_HUMAN | O43353
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RIPK2_HUMAN | O43353: 2n7z 2n83 4c8b 5ar2 5ar3 5ar4 5ar7 5ar8 5j79 5j7b 5ng0 5ng2 5ng3

(-) Related Entries Specified in the PDB File

5ar2 RIP2 KINASE CATALYTIC DOMAIN (1 - 310)
5ar3 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH AMP-PCP
5ar4 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH SB -203580
5ar7 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH BIARYL UREA
5ar8 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH BIPHENYLSULFONAMIDE