Structure of PDB 2r38 Chain A Binding Site BS01

Receptor Information
>2r38 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNVIGRNLLTQIGCTLNF
Ligand information
Ligand IDG4G
InChIInChI=1S/C32H33N5O6S2/c33-31(38)25-11-15-27(16-12-25)44(40,41)36(21-23-7-3-1-4-8-23)29-19-35-20-30(29)37(22-24-9-5-2-6-10-24)45(42,43)28-17-13-26(14-18-28)32(34)39/h1-18,29-30,35H,19-22H2,(H2,33,38)(H2,34,39)/t29-,30-/m0/s1
InChIKeySSQKDDJMCKLBOH-KYJUHHDHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[C@H]3CNC[C@@H]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(cc5)C(N)=O
CACTVS 3.341NC(=O)c1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[CH]3CNC[CH]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(cc5)C(N)=O
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN(C2CNCC2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)C(=O)N)S(=O)(=O)c5ccc(cc5)C(=O)N
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN([C@H]2CNC[C@@H]2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)C(=O)N)S(=O)(=O)c5ccc(cc5)C(=O)N
ACDLabs 10.04O=S(=O)(N(C3C(N(Cc1ccccc1)S(=O)(=O)c2ccc(C(=O)N)cc2)CNC3)Cc4ccccc4)c5ccc(C(=O)N)cc5
FormulaC32 H33 N5 O6 S2
Name4,4'-{(3S,4S)-PYRROLIDINE-3,4-DIYLBIS[(BENZYLIMINO)SULFONYL]}DIBENZAMIDE
ChEMBLCHEMBL1188505
DrugBank
ZINCZINC000024903340
PDB chain2r38 Chain B Residue 2501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2r38 Structural and Kinetic Analysis of Pyrrolidine-Based Inhibitors of the Drug-Resistant Ile84Val Mutant of HIV-1 Protease
Resolution1.81 Å
Binding residue
(original residue number in PDB)
D25 G27 A28 D29 D30 V32 G48 I50 V82
Binding residue
(residue number reindexed from 1)
D25 G27 A28 D29 D30 V32 G48 I50 V82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.44,Ki=0.036uM
Enzymatic activity
Catalytic site (original residue number in PDB) D25 T26 G27
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:2r38, PDBe:2r38, PDBj:2r38
PDBsum2r38
PubMed18692068
UniProtP04587|POL_HV1B5 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]