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CD38 structure-based inhibitor design using the N1-cyclic inosine 5'-diphosphate ribose template
Biology and Chemistry Report
3U4H
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text non-hydrolyzable inhibitor, two domains, cADPR cyclization, hydrolysis, 8-amino-N1-cIDPR, HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B
    Description ADP-ribosyl cyclase 1 
    Fragment extracellular domain, enzymatic domain 
    Mutation Q49T, N100D, N164D, N209D, N219D 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 30380.6 
    Source Method genetically manipulated  
    Entity Name Cyclic ADP-ribose hydrolase 1, cADPr hydrolase 1, T10 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    C8R  8-Amino-N1-Cyclic Inosine 5'-Diphosphoribose  C15 H21 N5 O14 P2   557.30  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B CD38_HUMAN O00121     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.4.99.20      
    A B  3.2.2.6      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    3953   Nad+ Nucleosidase Activity  Catalysis of the Reaction: Nad+ + H2o = Nicotinamide + Adp Ribose. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cd38
    Host Scientific Name Pichia pastoris  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    4 4p15 952     CD38 molecule CD38    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs77549972 LS-SNP   dbSNP   A 49 Q - > E Coil 75% (Exposed) 4 15780182
    rs140705952 LS-SNP   dbSNP   A 61 E - > V Helix 48% (Exposed) 4 15780219
    rs200465374 LS-SNP   dbSNP   A 62 T - > I Helix 21% (Intermediate) 4 15780222
    rs149195738 LS-SNP   dbSNP   A 114 T - > A Coil 65% (Exposed) 4 15818240
    rs145093502 LS-SNP   dbSNP   A 130 D - > H Helix 72% (Exposed) 4 15826528
    rs1800561 LS-SNP   dbSNP   A 140 R - > W Coil 76% (Exposed) 4 15826558
    rs199998792 LS-SNP   dbSNP   A 147 D - > G 3/10 Helix 26% (Intermediate) 4 15826580
    rs138866692 LS-SNP   dbSNP   A 148 T - > M Bend 10% (Intermediate) 4 15826583
    rs141827486 LS-SNP   dbSNP   A 175 D - > Y Coil 25% (Intermediate) 4 15835863
    rs201816957 LS-SNP   dbSNP   A 179 D - > G Turn 29% (Intermediate) 4 15835876
    rs75935397 LS-SNP   dbSNP   A 191 T - > M Helix 0% (Buried) 4 15835912
    rs150171847 LS-SNP   dbSNP   A 193 S - > C Helix 6% (Buried) 4 15835918 C8R
    rs138630257 LS-SNP   dbSNP   A 194 R - > H Helix 23% (Intermediate) 4 15835921
    rs200389163 LS-SNP   dbSNP   A 194 R - > C Helix 23% (Intermediate) 4 15835920
    rs201824472 LS-SNP   dbSNP   A 205 H - > N Beta Ladder 14% (Intermediate) 4 15839742
    rs149299047 LS-SNP   dbSNP   A 234 K - > N Turn 40% (Exposed) 4 15841691
    rs143575941 LS-SNP   dbSNP   A 251 R - > S Coil 64% (Exposed) 4 15842075
    rs201320129 LS-SNP   dbSNP   A 256 D - > E Bend 24% (Intermediate) 4 15842090
    rs147160884 LS-SNP   dbSNP   A 258 T - > I Helix 15% (Intermediate) 4 15842095
    rs201683843 LS-SNP   dbSNP   A 284 F - > C Helix 23% (Intermediate) 4 15850173