Structure of PDB 2rnf Chain B Binding Site BS01

Receptor Information
>2rnf Chain B (length=120) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNTFIHED
IWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIAS
TRRVVIACEGNPQVPVHFDG
Ligand information
Ligand IDUM3
InChIInChI=1S/C9H13N2O8P/c12-4-6-5(19-20(15,16)17)3-8(18-6)11-2-1-7(13)10-9(11)14/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyLXKGKXYIAAKOCT-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)CO)OP(=O)(O)O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)OP(=O)(O)O
CACTVS 3.341OC[CH]1O[CH](C[CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.341OC[C@H]1O[C@H](C[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2)CO
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 3'-MONOPHOSPHATE
ChEMBL
DrugBankDB03448
ZINCZINC000006524812
PDB chain2rnf Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2rnf The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H12 F42 N43 T44 H116 F117 G119
Binding residue
(residue number reindexed from 1)		H13 F43 N44 T45 H117 F118 G120
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H12 K40 H116 F117 D118
Catalytic site (residue number reindexed from 1) H13 K41 H117 F118 D119
Enzyme Commision number 3.1.27.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004519 endonuclease activity
GO:0004522 ribonuclease A activity
GO:0004540 RNA nuclease activity
Biological Process
GO:0019731 antibacterial humoral response
GO:0042742 defense response to bacterium
GO:0050830 defense response to Gram-positive bacterium
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2rnf, PDBe:2rnf, PDBj:2rnf
PDBsum2rnf
PubMed9878400
UniProtP34096|RNAS4_HUMAN Ribonuclease 4 (Gene Name=RNASE4)

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