Structure of PDB 1rds Chain A Binding Site BS01

Receptor Information
>1rds Chain A (length=105) Species: 5063 (Aspergillus phoenicis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESCEYTCGSTCYWSSDVSAAKAKGYSLYESGDTIDDYPHEYHDYEGFDFP
VSGTYYEYPIMSDYDVYTGGSPGADRVIFNGDDELAGVITHTGASGDDFV
ACSSS
Ligand information
Ligand IDGPC
InChIInChI=1S/C19H24FN8O11P/c20-9-13(6(3-29)37-16(9)28-5-23-10-14(28)25-18(22)26-15(10)32)39-40(34,35)36-4-7-11(30)12(31)17(38-7)27-2-1-8(21)24-19(27)33/h1-2,5-7,9,11-13,16-17,29-31H,3-4H2,(H,34,35)(H2,21,24,33)(H3,22,25,26,32)/t6-,7-,9-,11-,12-,13-,16-,17-/m1/s1
InChIKeyZSBUMMSBXYRQAK-FOJQSULLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)CO)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(=NC5=O)N)O)O)F)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CC(=NC5=O)N)O)O)F)N=C(NC2=O)N
ACDLabs 10.04O=C5NC(=Nc1c5ncn1C4OC(CO)C(OP(=O)(O)OCC3OC(N2C(=O)N=C(N)C=C2)C(O)C3O)C4F)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)N5C=CC(=NC5=O)N)[C@H]3F
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)N5C=CC(=NC5=O)N)[CH]3F
FormulaC19 H24 F N8 O11 P
Name2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE
ChEMBL
DrugBank
ZINCZINC000058631636
PDB chain1rds Chain A Residue 106 [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]
PDB1rds Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y37 H39 E40 Y41 H42 D43 Y44 E45 E57 P72 G73 R76 H91 G96 D97 F99
Binding residue
(residue number reindexed from 1)		Y37 H39 E40 Y41 H42 D43 Y44 E45 E57 P72 G73 R76 H91 G96 D97 F99
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y37 H39 E57 D75 R76 T90 H91 F99
Catalytic site (residue number reindexed from 1) Y37 H39 E57 D75 R76 T90 H91 F99
Enzyme Commision number 4.6.1.24: ribonuclease T1.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0004540 RNA nuclease activity
GO:0016829 lyase activity
GO:0046589 ribonuclease T1 activity

View graph for
Molecular Function
External links
PDB RCSB:1rds, PDBe:1rds, PDBj:1rds
PDBsum1rds
PubMed8218254
UniProtP00653|RNMS_ASPPH Guanyl-specific ribonuclease Ms

[Back to BioLiP]