Structure of PDB 2xyf Chain B Binding Site BS01

Receptor Information
>2xyf Chain B (length=99) Species: 11683 (Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF
Ligand information
Ligand IDG40
InChIInChI=1S/C38H53N5O6S/c1-36(2,3)30(32(44)39-7)40-34(46)38(48,23-26-13-10-9-11-14-26)20-12-21-43(42-33(45)31(37(4,5)6)41-35(47)49-8)24-27-15-17-28(18-16-27)29-19-22-50-25-29/h9-11,13-19,22,25,30-31,48H,12,20-21,23-24H2,1-8H3,(H,39,44)(H,40,46)(H,41,47)(H,42,45)/t30-,31-,38-/m1/s1
InChIKeyXNAIGGHDLWCRFU-SQQFMCCZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CC(C)(C)C(C(=O)NC)NC(=O)C(CCCN(Cc1ccc(cc1)c2ccsc2)NC(=O)C(C(C)(C)C)NC(=O)OC)(Cc3ccccc3)O
OpenEye OEToolkits 1.6.1CC(C)(C)[C@@H](C(=O)NC)NC(=O)[C@@](CCC[N@](Cc1ccc(cc1)c2ccsc2)NC(=O)[C@H](C(C)(C)C)NC(=O)OC)(Cc3ccccc3)O
CACTVS 3.352CNC(=O)[CH](NC(=O)[C](O)(CCCN(Cc1ccc(cc1)c2cscc2)NC(=O)[CH](NC(=O)OC)C(C)(C)C)Cc3ccccc3)C(C)(C)C
CACTVS 3.352CNC(=O)[C@@H](NC(=O)[C@@](O)(CCCN(Cc1ccc(cc1)c2cscc2)NC(=O)[C@@H](NC(=O)OC)C(C)(C)C)Cc3ccccc3)C(C)(C)C
FormulaC38 H53 N5 O6 S
Name
ChEMBLCHEMBL3221576
DrugBank
ZINCZINC000098208920
PDB chain2xyf Chain B Residue 1200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xyf HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L123 D125 G127 A128 D129 G148 G149 F153 P181 T182
Binding residue
(residue number reindexed from 1)		L23 D25 G27 A28 D29 G48 G49 F53 P81 T82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.44,Ki=3.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
Catalytic site (residue number reindexed from 1) D25 T26 G27
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:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:2xyf, PDBe:2xyf, PDBj:2xyf
PDBsum2xyf
PubMed
UniProtP12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)

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