Structure of PDB 3irx Chain A Binding Site BS01

Receptor Information
>3irx Chain A (length=555) Species: 11678 (Human immunodeficiency virus type 1 BH10) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAG
LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD
KLVSA
Ligand information
Ligand IDUDR
InChIInChI=1S/C27H29N3O5S/c1-15-11-18(13-21(24(15)33-5)26(31)36-6)20(9-7-8-10-23-29-28-17(3)34-23)19-12-16(2)25-22(14-19)30(4)27(32)35-25/h9,11-14H,7-8,10H2,1-6H3/b20-9+
InChIKeyOIXOQSQILWVOGS-AWQFTUOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1c(C)cc(cc1C(=O)SC)C(=CCCCc2oc(C)nn2)c3cc(C)c4OC(=O)N(C)c4c3
ACDLabs 11.02O=C(SC)c1c(OC)c(cc(c1)C(\c3cc2c(OC(=O)N2C)c(c3)C)=C/CCCc4nnc(o4)C)C
OpenEye OEToolkits 1.7.0Cc1cc(cc2c1OC(=O)N2C)C(=CCCCc3nnc(o3)C)c4cc(c(c(c4)C(=O)SC)OC)C
CACTVS 3.352COc1c(C)cc(cc1C(=O)SC)\C(=C/CCCc2oc(C)nn2)c3cc(C)c4OC(=O)N(C)c4c3
OpenEye OEToolkits 1.7.0Cc1cc(cc2c1OC(=O)N2C)/C(=C/CCCc3nnc(o3)C)/c4cc(c(c(c4)C(=O)SC)OC)C
FormulaC27 H29 N3 O5 S
Name(E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methy lbenzothioate;
S-methyl 5-[(1E)-1-(3,7-dimethyl-2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-en-1-yl]-2-methox y-3-methylbenzenecarbothioate
ChEMBLCHEMBL574823
DrugBank
ZINCZINC000034875798
PDB chain3irx Chain A Residue 556 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3irx Crystal Structure of HIV-1 reverse transcriptase (RT) in complex with the alkenyldiarylmethane (ADAM) Non-nucleoside RT Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methylbenzothioate.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		P95 L100 V106 V108 Y181 Y188 G190 F227 W229 L234
Binding residue
(residue number reindexed from 1)		P96 L101 V107 V109 Y182 Y189 G191 F228 W230 L235
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.00,IC50=1.0nM
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.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003964 RNA-directed DNA polymerase activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
Biological Process
GO:0006278 RNA-templated DNA biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3irx, PDBe:3irx, PDBj:3irx
PDBsum3irx
PubMed19775161
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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