Structure of PDB 3d8y Chain A Binding Site BS01

Receptor Information
>3d8y Chain A (length=124) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHES
LADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTT
QANKHIIVACEGNPYVPVHFDASV
Ligand information
Ligand IDT3S
InChIInChI=1S/C15H23N3O4/c1-10-8-18(15(21)16-14(10)20)13-7-11(19)12(22-13)9-17-5-3-2-4-6-17/h8,11-13,19H,2-7,9H2,1H3,(H,16,20,21)/t11-,12+,13+/m0/s1
InChIKeyGMOUOGHZJCSNOZ-YNEHKIRRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CN3CCCCC3)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CN3CCCCC3)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CN3CCCCC3
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CN3CCCCC3)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)CN3CCCCC3)O
FormulaC15 H23 N3 O4
Name5'-deoxy-5'-piperidin-1-ylthymidine
ChEMBLCHEMBL460910
DrugBankDB08596
ZINCZINC000040864131
PDB chain3d8y Chain A Residue 127 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3d8y Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation
Resolution1.72 Å
Binding residue
(original residue number in PDB)		K41 V43 N44 T45 F120
Binding residue
(residue number reindexed from 1)		K41 V43 N44 T45 F120
Annotation score1
Binding affinityMOAD: Ki=396uM
PDBbind-CN: -logKd/Ki=3.40,Ki=396uM
BindingDB: Ki=396000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H12 K41 H119 F120 D121
Catalytic site (residue number reindexed from 1) H12 K41 H119 F120 D121
Enzyme Commision number 4.6.1.18: pancreatic ribonuclease.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004519 endonuclease activity
GO:0004522 ribonuclease A activity
GO:0004540 RNA nuclease activity
GO:0005515 protein binding
GO:0016829 lyase activity
Biological Process
GO:0050830 defense response to Gram-positive bacterium
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3d8y, PDBe:3d8y, PDBj:3d8y
PDBsum3d8y
PubMed19173562
UniProtP61823|RNAS1_BOVIN Ribonuclease pancreatic (Gene Name=RNASE1)

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