Structure of PDB 3ndx Chain A Binding Site BS01

Receptor Information
>3ndx 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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDRIT
InChIInChI=1S/C37H48N6O5S2/c1-24(2)33(42-36(46)43(5)20-29-22-49-35(40-29)25(3)4)34(45)39-28(16-26-12-8-6-9-13-26)18-32(44)31(17-27-14-10-7-11-15-27)41-37(47)48-21-30-19-38-23-50-30/h6-15,19,22-25,28,31-33,44H,16-18,20-21H2,1-5H3,(H,39,45)(H,41,47)(H,42,46)/t28-,31-,32-,33-/m0/s1
InChIKeyNCDNCNXCDXHOMX-XGKFQTDJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C)c1nc(cs1)CN(C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](Cc2ccccc2)C[C@@H]([C@H](Cc3ccccc3)NC(=O)OCc4cncs4)O
OpenEye OEToolkits 1.7.0CC(C)c1nc(cs1)CN(C)C(=O)NC(C(C)C)C(=O)NC(Cc2ccccc2)CC(C(Cc3ccccc3)NC(=O)OCc4cncs4)O
CACTVS 3.370CC(C)[CH](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)N[CH](C[CH](O)[CH](Cc2ccccc2)NC(=O)OCc3scnc3)Cc4ccccc4
CACTVS 3.370CC(C)[C@H](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)N[C@H](C[C@H](O)[C@H](Cc2ccccc2)NC(=O)OCc3scnc3)Cc4ccccc4
ACDLabs 12.01O=C(OCc1scnc1)NC(Cc2ccccc2)C(O)CC(NC(=O)C(NC(=O)N(Cc3nc(sc3)C(C)C)C)C(C)C)Cc4ccccc4
FormulaC37 H48 N6 O5 S2
NameRITONAVIR;
A-84538
ChEMBLCHEMBL163
DrugBankDB00503
ZINCZINC000003944422
PDB chain3ndx Chain A Residue 100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ndx Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures
Resolution1.03 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 A28 D29 G48 I50 P81 V82
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 G48 I50 P81 V82
Annotation score1
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:3ndx, PDBe:3ndx, PDBj:3ndx
PDBsum3ndx
PubMed
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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