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 3d1x Chain A Binding Site BS01

Receptor Information
>3d1x Chain A (length=99) Species: 11682 (Human immunodeficiency virus type 1 (BH5 ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFMKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDROC
InChIInChI=1S/C38H50N6O5/c1-38(2,3)43-37(49)32-20-26-14-7-8-15-27(26)22-44(32)23-33(45)30(19-24-11-5-4-6-12-24)41-36(48)31(21-34(39)46)42-35(47)29-18-17-25-13-9-10-16-28(25)40-29/h4-6,9-13,16-18,26-27,30-33,45H,7-8,14-15,19-23H2,1-3H3,(H2,39,46)(H,41,48)(H,42,47)(H,43,49)/t26-,27+,30-,31-,32-,33+/m0/s1
InChIKeyQWAXKHKRTORLEM-UGJKXSETSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(N)CC(NC(=O)c1nc2c(cc1)cccc2)C(=O)NC(Cc3ccccc3)C(O)CN5C(C(=O)NC(C)(C)C)CC4C(CCCC4)C5
OpenEye OEToolkits 1.7.0CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2C[N@]1C[C@H]([C@H](Cc3ccccc3)NC(=O)[C@H](CC(=O)N)NC(=O)c4ccc5ccccc5n4)O
OpenEye OEToolkits 1.7.0CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(C(Cc3ccccc3)NC(=O)C(CC(=O)N)NC(=O)c4ccc5ccccc5n4)O
CACTVS 3.370CC(C)(C)NC(=O)[CH]1C[CH]2CCCC[CH]2CN1C[CH](O)[CH](Cc3ccccc3)NC(=O)[CH](CC(N)=O)NC(=O)c4ccc5ccccc5n4
CACTVS 3.370CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc3ccccc3)NC(=O)[C@H](CC(N)=O)NC(=O)c4ccc5ccccc5n4
FormulaC38 H50 N6 O5
Name(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide;
Fortovase;
SAQUINAVIR;
RO 31-8959
ChEMBLCHEMBL114
DrugBankDB01232
ZINCZINC000003914596
PDB chain3d1x Chain A Residue 201 [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]
PDB3d1x Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.
Resolution1.05 Å
Binding residue
(original residue number in PDB)
D25 G27 D29 D30 G48 G49 I50 I84
Binding residue
(residue number reindexed from 1)
D25 G27 D29 D30 G48 G49 I50 I84
Annotation score1
Binding affinityMOAD: Ki=2.2nM
PDBbind-CN: -logKd/Ki=8.66,Ki=2.2nM
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:3d1x, PDBe:3d1x, PDBj:3d1x
PDBsum3d1x
PubMed18597780
UniProtP04587|POL_HV1B5 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]

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