Structure of PDB 3ckt Chain A Binding Site BS01

Receptor Information
>3ckt 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
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 D29 D30 G48 G49 I50 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 G49 I50 I84
Annotation score1
Binding affinityMOAD: Ki=0.48uM
PDBbind-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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