Structure of PDB 3djp Chain B Binding Site BS01

Receptor Information
>3djp Chain B (length=124) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KESAAAKFERQHMDSGNSPSSSSNYCNLMMCCRKMTQGKCKPVNTFVHES
LADVKAVCSQKKVTCKNGQTNCYQSKSTMRITDCRETGSSKYPNCAYKTT
QVEKHIIVACGGKPSVPVHFDASV
Ligand information
Ligand IDUA3
InChIInChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6+,7-,8-/m1/s1
InChIKeyFOGRQMPFHUHIGU-PXBUCIJWSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H](C(O2)CO)OP(=O)(O)O)O
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.341OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURACIL ARABINOSE-3'-PHOSPHATE;
1-(3-O-PHOSPHONO-BETA-L-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE
ChEMBLCHEMBL460901
DrugBankDB02805
ZINC
PDB chain3djp Chain B Residue 201 [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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PDB3djp Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors
Resolution1.6 Å
Binding residue
(original residue number in PDB)		V43 N44 T45 H119 F120
Binding residue
(residue number reindexed from 1)		V43 N44 T45 H119 F120
Annotation score1
Binding affinityMOAD: Ki=63.2uM
PDBbind-CN: -logKd/Ki=4.20,Ki=63.2uM
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:0016829 lyase activity
GO:0042802 identical protein binding
Biological Process
GO:0050830 defense response to Gram-positive bacterium
GO:0051607 defense response to virus
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3djp, PDBe:3djp, PDBj:3djp
PDBsum3djp
PubMed19643512
UniProtP00669|RNS_BOVIN Seminal ribonuclease (Gene Name=SRN)

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