Structure of PDB 1af2 Chain A Binding Site BS02

Receptor Information
>1af2 Chain A (length=294) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHPRFQTAFAQLADNLQSALEPILADKYFPALLTGEQVSSLKSATGLDED
ALAFALLPLAAACARTPLSNFNVGAIARGVSGTWYFGANMEFIGATMQQT
VHAEQSAISHAWLSGEKALAAITVNYTPCGHCRQFMNELNSGLDLRIHLP
GREAHALRDYLPDAFGPKDLEIKTLLMDEQDHGYALTGDALSQAAIAAAN
RSHMPYSKSPSGVALECKDGRIFSGSYAENAAFNPTLPPLQGALILLNLK
GYDYPDIQRAVLAEKADAPLIQWDATSATLKALGCHSIDRVLLA
Ligand information
Ligand IDU
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain1af2 Chain A Residue 295 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1af2 The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N89 E91 H102 E104 P128 C129
Binding residue
(residue number reindexed from 1)		N89 E91 H102 E104 P128 C129
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.10,Ki=0.8mM
Enzymatic activity
Catalytic site (original residue number in PDB) H102 E104 C129 C132
Catalytic site (residue number reindexed from 1) H102 E104 C129 C132
Enzyme Commision number 3.5.4.5: cytidine deaminase.
Gene Ontology
Molecular Function
GO:0001884 pyrimidine nucleoside binding
GO:0003824 catalytic activity
GO:0004126 cytidine deaminase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006217 deoxycytidine catabolic process
GO:0009972 cytidine deamination
GO:0015949 nucleobase-containing small molecule interconversion
GO:0055086 nucleobase-containing small molecule metabolic process
GO:0072527 pyrimidine-containing compound metabolic process
GO:1901135 carbohydrate derivative metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1af2, PDBe:1af2, PDBj:1af2
PDBsum1af2
PubMed9125497
UniProtP0ABF6|CDD_ECOLI Cytidine deaminase (Gene Name=cdd)

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