Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA FASPR EM-Refiner GPU-I-TASSER

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14

BioLiP

Structure of PDB 6oy0 Chain B Binding Site BS01

Receptor Information
>6oy0 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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDNJ7
InChIInChI=1S/C30H42N2O9S/c1-3-20(2)16-32(42(37,38)23-11-9-22(10-12-23)27(35)18-33)17-26(34)25(15-21-7-5-4-6-8-21)31-30(36)41-28-19-40-29-24(28)13-14-39-29/h4-12,20,24-29,33-35H,3,13-19H2,1-2H3,(H,31,36)/t20-,24-,25-,26+,27+,28-,29+/m0/s1
InChIKeyZFBZVUBZCNSMDT-JTBOUOTJSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(C(Cc1ccccc1)NC(OC2C3C(OC2)OCC3)=O)(CN(CC(C)CC)S(c4ccc(cc4)C(CO)O)(=O)=O)O
OpenEye OEToolkits 2.0.7CCC(C)CN(CC(C(Cc1ccccc1)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc(cc4)C(CO)O
OpenEye OEToolkits 2.0.7CC[C@H](C)CN(C[C@H]([C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc(cc4)[C@@H](CO)O
CACTVS 3.385CC[CH](C)CN(C[CH](O)[CH](Cc1ccccc1)NC(=O)O[CH]2CO[CH]3OCC[CH]23)[S](=O)(=O)c4ccc(cc4)[CH](O)CO
CACTVS 3.385CC[C@H](C)CN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[S](=O)(=O)c4ccc(cc4)[C@H](O)CO
FormulaC30 H42 N2 O9 S
Name(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{({4-[(1S)-1,2-dihydroxyethyl]phenyl}sulfonyl)[(2S)-2-methylbutyl]amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate
ChEMBLCHEMBL4552821
DrugBank
ZINC
PDB chain6oy0 Chain A Residue 103 [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]
PDB6oy0 HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
D25 A28 D29 D30 I47 G48 L76 P81 V82 I84
Binding residue
(residue number reindexed from 1)
D25 A28 D29 D30 I47 G48 L76 P81 V82 I84
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.30,Ki=0.504nM
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:6oy0, PDBe:6oy0, PDBj:6oy0
PDBsum6oy0
PubMed31386368
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417