Structure of PDB 3t1a Chain A Binding Site BS01

Receptor Information
>3t1a Chain A (length=554) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKN
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIR
Ligand information
Ligand ID5MA
InChIInChI=1S/C20H14Cl3N7O/c21-11-6-10(8-24)17(23)16(7-11)31-19-13(22)3-4-15-18(19)27-29-30(15)9-14-12-2-1-5-25-20(12)28-26-14/h1-7H,8-9,24H2,(H,25,26,28)
InChIKeyCUYHWBGVPXGMKQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCc1cc(Cl)cc(Oc2c(Cl)ccc3n(Cc4[nH]nc5ncccc45)nnc23)c1Cl
ACDLabs 12.01Clc5cc(Oc4c(Cl)ccc1c4nnn1Cc2c3cccnc3nn2)c(Cl)c(c5)CN
OpenEye OEToolkits 1.7.2c1cc2c([nH]nc2nc1)Cn3c4ccc(c(c4nn3)Oc5cc(cc(c5Cl)CN)Cl)Cl
FormulaC20 H14 Cl3 N7 O
Name1-(2,5-dichloro-3-{[5-chloro-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1H-benzotriazol-4-yl]oxy}phenyl)methanamine
ChEMBLCHEMBL1939501
DrugBank
ZINCZINC000073240563
PDB chain3t1a Chain A Residue 561 [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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PDB3t1a Design and synthesis of conformationally constrained inhibitors of non-nucleoside reverse transcriptase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		P95 L100 K101 N103 V106 V108 Y181 Y188 V189 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		P92 L97 K98 N100 V103 V105 Y178 Y185 V186 F224 W226 L231 H232 P233 Y315
Annotation score1
Binding affinityMOAD: Ki=4.3nM
PDBbind-CN: -logKd/Ki=8.37,Ki=4.3nM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3t1a, PDBe:3t1a, PDBj:3t1a
PDBsum3t1a
PubMed21985673
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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