Structure of PDB 3ckt Chain B Binding Site BS01

Receptor Information
>3ckt Chain B (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
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDYDP
InChIInChI=1S/C28H37N5O6S2/c1-19(2)13-15-32(40(36,37)23-9-5-21(6-10-23)27(29)34)25-17-31-18-26(25)33(16-14-20(3)4)41(38,39)24-11-7-22(8-12-24)28(30)35/h5-14,25-26,31H,15-18H2,1-4H3,(H2,29,34)(H2,30,35)/t25-,26-/m0/s1
InChIKeySNNQNFFJBMXSFD-UIOOFZCWSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=S(=O)(N(C2C(N(C\C=C(/C)C)S(=O)(=O)c1ccc(C(=O)N)cc1)CNC2)C\C=C(/C)C)c3ccc(C(=O)N)cc3
CACTVS 3.341CC(C)=CCN([CH]1CNC[CH]1N(CC=C(C)C)[S](=O)(=O)c2ccc(cc2)C(N)=O)[S](=O)(=O)c3ccc(cc3)C(N)=O
OpenEye OEToolkits 1.5.0CC(=CCN(C1CNCC1N(CC=C(C)C)S(=O)(=O)c2ccc(cc2)C(=O)N)S(=O)(=O)c3ccc(cc3)C(=O)N)C
OpenEye OEToolkits 1.5.0CC(=CCN([C@H]1CNC[C@@H]1N(CC=C(C)C)S(=O)(=O)c2ccc(cc2)C(=O)N)S(=O)(=O)c3ccc(cc3)C(=O)N)C
CACTVS 3.341CC(C)=CCN([C@H]1CNC[C@@H]1N(CC=C(C)C)[S](=O)(=O)c2ccc(cc2)C(N)=O)[S](=O)(=O)c3ccc(cc3)C(N)=O
FormulaC28 H37 N5 O6 S2
Name(3S,4S),-3,4-Bis-[(4-carbamoyl-benzensulfonyl)-(3-methyl-but-2-enyl)-amino]-pyrrolidine
ChEMBL
DrugBank
ZINCZINC000058639096
PDB chain3ckt Chain A Residue 2501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ckt Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors
Resolution1.65 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D30 G48
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D30 G48
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.32,Ki=0.48uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3ckt, PDBe:3ckt, PDBj:3ckt
PDBsum3ckt
PubMed21762812
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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