Structure of PDB 3d8z Chain A Binding Site BS01

Receptor Information
>3d8z 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 IDTXS
InChIInChI=1S/C14H21N3O4/c1-9-7-17(14(20)15-13(9)19)12-6-10(18)11(21-12)8-16-4-2-3-5-16/h7,10-12,18H,2-6,8H2,1H3,(H,15,19,20)/t10-,11+,12+/m1/s1
InChIKeyXUSBTLVYPZUOAW-WOPDTQHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([C@@H]2C[C@@H](O)[C@H](CN3CCCC3)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CN3CCCC3)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CN3CCCC3
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)CN3CCCC3)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)CN3CCCC3)O
FormulaC14 H21 N3 O4
Name1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione;
5'-deoxy-5'-pyrrolidin-1-ylthymidine
ChEMBL
DrugBankDB08661
ZINCZINC000053683282
PDB chain3d8z Chain A Residue 125 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3d8z Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation
Resolution1.98 Å
Binding residue
(original residue number in PDB)		H12 V43 N44 T45 H119 F120
Binding residue
(residue number reindexed from 1)		H12 V43 N44 T45 H119 F120
Annotation score1
Binding affinityMOAD: Ki=423uM
PDBbind-CN: -logKd/Ki=3.37,Ki=423uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3d8z, PDBe:3d8z, PDBj:3d8z
PDBsum3d8z
PubMed19173562
UniProtP61823|RNAS1_BOVIN Ribonuclease pancreatic (Gene Name=RNASE1)

[Back to BioLiP]