Structure of PDB 5zdn Chain A Binding Site BS01

Receptor Information
>5zdn Chain A (length=192) Species: 1906 (Streptomyces fradiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFAFGAVVERRDELDGRPWISYPVRVVADTPELVAVHLSHGTRLTFGDDP
FSWGPHPWQLFGDRWQSAGILQLHRPGRGHSVWVLRDADTGAFREWYVNV
EAPWRRTPTGFSTLDHEIDLVVPADSRTFRWKDVEKFEERARIGHFSPEE
ATAIRAEAADVAREIAAGEQWWDTRWSRWEPPAGWNALLQSF
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain5zdn Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5zdn Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.
Resolution2.02 Å
Binding residue
(original residue number in PDB)		W68 F71 W75 Q76 S77 K142
Binding residue
(residue number reindexed from 1)		W58 F61 W65 Q66 S67 K132
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5zdn, PDBe:5zdn, PDBj:5zdn
PDBsum5zdn
PubMed30010320
UniProtD2SNF7|FOMD_STRFR Cytidylyl-2-hydroxypropylphosphonate hydrolase (Gene Name=fomD)

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