Structure of PDB 1gnn Chain B Binding Site BS01

Receptor Information
>1gnn 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
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPNNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDU0E
InChIInChI=1S/C28H52N8O6/c1-16(2)19(15-23(38)22(34-17(3)37)14-18-8-5-4-6-9-18)26(41)36-21(11-12-24(29)39)27(42)35-20(25(30)40)10-7-13-33-28(31)32/h16,18-23,38H,4-15H2,1-3H3,(H2,29,39)(H2,30,40)(H,34,37)(H,35,42)(H,36,41)(H4,31,32,33)/t19-,20-,21-,22-,23-/m0/s1
InChIKeyXTOQWMLQBSGKOK-VUBDRERZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)[CH](C[CH](O)[CH](CC1CCCCC1)NC(C)=O)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=N)C(N)=O
OpenEye OEToolkits 1.5.0CC(C)C(CC(C(CC1CCCCC1)NC(=O)C)O)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=N)N)C(=O)N
OpenEye OEToolkits 1.5.0CC(C)[C@H](C[C@@H]([C@H](CC1CCCCC1)NC(=O)C)O)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N
CACTVS 3.341CC(C)[C@H](C[C@H](O)[C@H](CC1CCCCC1)NC(C)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=N)C(N)=O
ACDLabs 10.04O=C(N)C(NC(=O)C(NC(=O)C(C(C)C)CC(O)C(NC(=O)C)CC1CCCCC1)CCC(=O)N)CCCNC(=[N@H])N
FormulaC28 H52 N8 O6
NameN-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE
ChEMBL
DrugBank
ZINC
PDB chain1gnn Chain A Residue 100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1gnn Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 I47 G48 I50 P81 N82
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 I47 G48 I50 P81 N82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.68,Ki=2100nM
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
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Biological Process
External links
PDB RCSB:1gnn, PDBe:1gnn, PDBj:1gnn
PDBsum1gnn
PubMed8718851
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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