Structure of PDB 1ody Chain A Binding Site BS01

Receptor Information
>1ody Chain A (length=99) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGAWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDLP1
InChIInChI=1S/C45H58N6O7/c1-7-35(43(56)50-37(42(46)55)23-31-18-12-16-29-14-8-10-20-33(29)31)48-40(54)25-39(53)36(22-26(2)3)49-45(58)41(27(4)5)51-44(57)38(47-28(6)52)24-32-19-13-17-30-15-9-11-21-34(30)32/h8-21,26-27,35-39,41,53H,7,22-25H2,1-6H3,(H2,46,55)(H,47,52)(H,48,54)(H,49,58)(H,50,56)(H,51,57)/t35-,36-,37-,38-,39-,41-/m0/s1
InChIKeyACPDNLLISIAERE-ZYWZKTPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCC(C(=O)NC(Cc1cccc2c1cccc2)C(=O)N)NC(=O)CC(C(CC(C)C)NC(=O)C(C(C)C)NC(=O)C(Cc3cccc4c3cccc4)NC(=O)C)O
OpenEye OEToolkits 1.5.0CC[C@@H](C(=O)N[C@@H](Cc1cccc2c1cccc2)C(=O)N)NC(=O)C[C@@H]([C@H](CC(C)C)NC(=O)[C@H](C(C)C)NC(=O)[C@H](Cc3cccc4c3cccc4)NC(=O)C)O
CACTVS 3.341CC[CH](NC(=O)C[CH](O)[CH](CC(C)C)NC(=O)[CH](NC(=O)[CH](Cc1cccc2ccccc12)NC(C)=O)C(C)C)C(=O)N[CH](Cc3cccc4ccccc34)C(N)=O
ACDLabs 10.04O=C(N)C(NC(=O)C(NC(=O)CC(O)C(NC(=O)C(NC(=O)C(NC(=O)C)Cc2cccc1ccccc12)C(C)C)CC(C)C)CC)Cc4c3ccccc3ccc4
CACTVS 3.341CC[C@H](NC(=O)C[C@H](O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@H](Cc1cccc2ccccc12)NC(C)=O)C(C)C)C(=O)N[C@@H](Cc3cccc4ccccc34)C(N)=O
FormulaC45 H58 N6 O7
Name4-[2-(2-ACETYLAMINO-3-NAPHTALEN-1-YL-PROPIONYLAMINO)-4-METHYL-PENTANOYLAMINO]-3-HYDROXY-6-METHYL-HEPTANOIC ACID [1-(1-CARBAMOYL-2-NAPHTHALEN-1-YL-ETHYLCARBAMOYL)-PROPYL]-AMIDE
ChEMBL
DrugBank
ZINCZINC000085533286
PDB chain1ody 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]
PDB1ody Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 I47 G48 G49 P81 V82 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 I47 G48 G49 P81 V82 I84
Annotation score1
Binding affinityMOAD: Ki=8nM
PDBbind-CN: -logKd/Ki=8.10,Ki=8nM
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:1ody, PDBe:1ody, PDBj:1ody
PDBsum1ody
PubMed9827997
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]