Structure of PDB 4g8l Chain A Binding Site BS01

Receptor Information
>4g8l Chain A (length=307) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSGRRAAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHN
AVQMSREDIVELLLRHGADPVLRKKNGATPFILAAIAGSVKLLKLFLSKG
ADVNECDFYGFTAFMEAAVYGKVKALKFLYKRGANVNLRRKTKEDQERLR
GATALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSD
VEAITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEIN
DTDSDGKTALLLAVELKLKKIAELLCKRGASTCGDLVMTARRNYDHSLVK
VLLSHGA
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 chain4g8l Chain A Residue 401 [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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PDB4g8l Innate Immune Messenger 2-5A Tethers Human RNase L into Active High-Order Complexes.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		E55 E57 G58 W60 Q68 K89 Y124 F126 E131 Y135 R155
Binding residue
(residue number reindexed from 1)		E40 E42 G43 W45 Q53 K74 Y109 F111 E116 Y120 R140
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.00,Kd=10nM
BindingDB: IC50=20nM,EC50=0.210000nM
Enzymatic activity
Enzyme Commision number 3.1.26.-
External links
PDB RCSB:4g8l, PDBe:4g8l, PDBj:4g8l
PDBsum4g8l
PubMed23084743
UniProtQ05823|RN5A_HUMAN 2-5A-dependent ribonuclease (Gene Name=RNASEL)

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