Structure of PDB 3oyn Chain A Binding Site BS06

Receptor Information
>3oyn Chain A (length=368) Species: 11963 (Human spumaretrovirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNK
ASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYP
TKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLE
FSTPYHPQSSGKVERKHSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTY
SPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPST
PPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQ
Ligand information
Ligand IDZZX
InChIInChI=1S/C21H21ClFN5O4/c1-4-26-8-10(2)28-16-14(18(29)17(28)21(26)32)20(31)27(25-15(16)19(30)24-3)9-11-5-6-13(23)12(22)7-11/h5-7,10,29H,4,8-9H2,1-3H3,(H,24,30)/t10-/m0/s1
InChIKeyJSRREMIKIHJGAA-JTQLQIEISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCN1C[C@@H](n2c3c(c(c2C1=O)O)C(=O)N(N=C3C(=O)NC)Cc4ccc(c(c4)Cl)F)C
OpenEye OEToolkits 1.7.0CCN1CC(n2c3c(c(c2C1=O)O)C(=O)N(N=C3C(=O)NC)Cc4ccc(c(c4)Cl)F)C
CACTVS 3.370CCN1C[C@H](C)n2c(c(O)c3C(=O)N(Cc4ccc(F)c(Cl)c4)N=C(C(=O)NC)c23)C1=O
CACTVS 3.370CCN1C[CH](C)n2c(c(O)c3C(=O)N(Cc4ccc(F)c(Cl)c4)N=C(C(=O)NC)c23)C1=O
ACDLabs 12.01Fc1ccc(cc1Cl)CN4N=C(c3n2c(C(=O)N(CC2C)CC)c(O)c3C4=O)C(=O)NC
FormulaC21 H21 Cl F N5 O4
Name(6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide
ChEMBLCHEMBL1237018
DrugBank
ZINCZINC000035801891
PDB chain3oyn Chain A Residue 398 [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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PDB3oyn Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		D128 D185 P214 E221
Binding residue
(residue number reindexed from 1)		D121 D178 P207 E214
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.60,IC50=25nM
Enzymatic activity
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.26.4: ribonuclease H.
3.4.23.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
Biological Process
GO:0015074 DNA integration

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3oyn, PDBe:3oyn, PDBj:3oyn
PDBsum3oyn
PubMed21030679
UniProtP14350|POL_FOAMV Pro-Pol polyprotein (Gene Name=pol)

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