Structure of PDB 3klf Chain M Binding Site BS05

Receptor Information
>3klf Chain M (length=553) 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]
ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQ
GWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTK
IEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDS
WTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAEL
ELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKT
GKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETW
WTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETK
LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQY
ALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKL
VSA
Ligand information
Ligand IDZP4
InChIInChI=1S/C20H28N10O19P4/c1-8-3-29(20(34)26-18(8)33)12-2-9(27-28-22)10(45-12)4-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-5-11-14(31)15(32)19(46-11)30-7-25-13-16(21)23-6-24-17(13)30/h3,6-7,9-12,14-15,19,31-32H,2,4-5H2,1H3,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,24)(H,26,33,34)/t9-,10+,11+,12+,14+,15+,19+/m0/s1
InChIKeyNHJROJSMKQZWCP-SLFMBYJQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-]
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-]
FormulaC20 H28 N10 O19 P4
Name
ChEMBL
DrugBank
ZINCZINC000263620792
PDB chain3klf Chain M Residue 823 [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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PDB3klf Structural basis of HIV-1 resistance to AZT by excision.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		K65 R72 D110 D113 A114 Y115 F116 Q151 M184 D185 K219
Binding residue
(residue number reindexed from 1)		K64 R71 D109 D112 A113 Y114 F115 Q150 M183 D184 K218
Annotation score1
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
View graph for
Biological Process
External links
PDB RCSB:3klf, PDBe:3klf, PDBj:3klf
PDBsum3klf
PubMed20852643
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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