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Receptor Information

>3kdb Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand ID

006

InChI

InChI=1S/C35H41N3O6S/c1-21-11-10-12-22(2)31(21)44-19-28(40)36-26(17-23-13-6-5-7-14-23)30(41)34(43)38-20-45-35(3,4)32(38)33(42)37-29-25-16-9-8-15-24(25)18-27(29)39/h5-16,26-27,29-30,32,39,41H,17-20H2,1-4H3,(H,36,40)(H,37,42)/t26-,27+,29-,30-,32+/m0/s1

InChIKey

KKTYZYHUPKXLPL-RIQJEONASA-N

SMILES

Software	SMILES
CACTVS 3.370	Cc1cccc(C)c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](O)C(=O)N3CSC(C)(C)[C@H]3C(=O)N[C@@H]4[C@H](O)Cc5ccccc45
ACDLabs 12.01	O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)COc3c(cccc3C)C)Cc4ccccc4)CSC5(C)C
CACTVS 3.370	Cc1cccc(C)c1OCC(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45
OpenEye OEToolkits 1.7.0	Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C
OpenEye OEToolkits 1.7.0	Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C

Formula

C35 H41 N3 O6 S

Name

(4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
KNI-10006

PDB chain

3kdb Chain B Residue 100 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3kdb How much binding affinity can be gained by filling a cavity?
Resolution	1.66 Å
Binding residue (original residue number in PDB)	D25 G27 A28 D29 D30 I47 G49 I50 I84
Binding residue (residue number reindexed from 1)	D25 G27 A28 D29 D30 I47 G49 I50 I84
Annotation score	1
Binding affinity	MOAD: Kd=0.14nM PDBbind-CN: -logKd/Ki=9.85,Kd=0.14nM

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.

	Molecular Function
GO:0004190	aspartic-type endopeptidase activity

	Biological Process
GO:0006508	proteolysis

PDB	RCSB:3kdb, PDBe:3kdb, PDBj:3kdb
PDBsum	3kdb
PubMed	20028396
UniProt	P03367\|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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Structure of PDB 3kdb Chain B Binding Site BS01