Structure of PDB 1wdy Chain A Binding Site BS01

Receptor Information
>1wdy Chain A (length=285) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHNAVQMS
REDIVELLLRHGADPVLRKKNGATPFLLAAIAGSVKLLKLFLSKGADVNE
CDFYGFTAFMEAAVYGKVKALKFLYKRGANVNLRRKTKEDQERLRKGGAT
ALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSDVEA
ITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTD
SDGKTALLLAVELKLKKIAELLCKRGASTDCGDLV
Ligand information
Ligand ID25A
InChIInChI=1S/C30H38N15O19P3/c31-22-13-25(37-4-34-22)43(7-40-13)28-19(49)16(46)10(60-28)2-58-66(53,54)64-21-18(48)12(62-30(21)45-9-42-15-24(33)36-6-39-27(15)45)3-59-67(55,56)63-20-17(47)11(1-57-65(50,51)52)61-29(20)44-8-41-14-23(32)35-5-38-26(14)44/h4-12,16-21,28-30,46-49H,1-3H2,(H,53,54)(H,55,56)(H2,31,34,37)(H2,32,35,38)(H2,33,36,39)(H2,50,51,52)/t10-,11-,12-,16-,17-,18-,19-,20-,21-,28-,29-,30-/m1/s1
InChIKeySIIZPVYVXNXXQG-UQTMIEBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5ncnc6N)CO[P@@](=O)(O)O[C@@H]7[C@@H]([C@H](O[C@H]7n8cnc9c8ncnc9N)COP(=O)(O)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[C@@H]4[C@H](O)[C@@H](CO[P@](O)(=O)O[C@@H]5[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]5n6cnc7c(N)ncnc67)O[C@H]4n8cnc9c(N)ncnc89)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5ncnc6N)COP(=O)(O)OC7C(C(OC7n8cnc9c8ncnc9N)COP(=O)(O)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](O)[CH](CO[P](O)(=O)O[CH]5[CH](O)[CH](CO[P](O)(O)=O)O[CH]5n6cnc7c(N)ncnc67)O[CH]4n8cnc9c(N)ncnc89)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OCC9OC(n1c2ncnc(N)c2nc1)C(OP(=O)(O)OCC8OC(n4cnc3c(ncnc34)N)C(OP(=O)(O)OCC7OC(n5c6ncnc(N)c6nc5)C(O)C7O)C8O)C9O
FormulaC30 H38 N15 O19 P3
Name5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE
ChEMBLCHEMBL414948
DrugBank
ZINC
PDB chain1wdy Chain A Residue 1001 [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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PDB1wdy Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E55 W60 Q68 K89 Y124 F126 E131 Y135 R155
Binding residue
(residue number reindexed from 1)		E35 W40 Q48 K69 Y104 F106 E111 Y115 R135
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.89,IC50=13nM
BindingDB: IC50=20nM,EC50=0.210000nM
Enzymatic activity
Enzyme Commision number 3.1.26.-
External links
PDB RCSB:1wdy, PDBe:1wdy, PDBj:1wdy
PDBsum1wdy
PubMed15385955
UniProtQ05823|RN5A_HUMAN 2-5A-dependent ribonuclease (Gene Name=RNASEL)

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