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Receptor Information

>3kdd Chain A (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

JZQ

InChI

InChI=1S/C33H35F2N3O6S/c1-33(2)30(31(42)37-27-21-12-7-6-11-20(21)16-25(27)39)38(18-45-33)32(43)28(41)24(15-19-9-4-3-5-10-19)36-26(40)17-44-29-22(34)13-8-14-23(29)35/h3-14,24-25,27-28,30,39,41H,15-18H2,1-2H3,(H,36,40)(H,37,42)/t24-,25+,27-,28-,30+/m0/s1

InChIKey

KCNWMHBIZSWXTB-UPZHSWQNSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)COc3c(cccc3F)F)O)C(=O)N[C@H]4c5ccccc5C[C@H]4O)C
ACDLabs 12.01	O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)COc3c(F)cccc3F)Cc4ccccc4)CSC5(C)C
CACTVS 3.370	CC1(C)SCN([C@@H]1C(=O)N[C@@H]2[C@H](O)Cc3ccccc23)C(=O)[C@@H](O)[C@H](Cc4ccccc4)NC(=O)COc5c(F)cccc5F
CACTVS 3.370	CC1(C)SCN([CH]1C(=O)N[CH]2[CH](O)Cc3ccccc23)C(=O)[CH](O)[CH](Cc4ccccc4)NC(=O)COc5c(F)cccc5F
OpenEye OEToolkits 1.7.0	CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)COc3c(cccc3F)F)O)C(=O)NC4c5ccccc5CC4O)C

Formula

C33 H35 F2 N3 O6 S

Name

(4R)-3-[(2S,3S)-3-{[(2,6-difluorophenoxy)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-10265

PDB chain

3kdd 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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Structure summary

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PDB	3kdd How much binding affinity can be gained by filling a cavity?
Resolution	1.8 Å
Binding residue (original residue number in PDB)	R8 D25 G27 A28 D29 G49 I50 I84
Binding residue (residue number reindexed from 1)	R8 D25 G27 A28 D29 G49 I50 I84
Annotation score	1
Binding affinity	MOAD: Kd=3.45nM PDBbind-CN: -logKd/Ki=8.46,Kd=3.45nM

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

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Structure of PDB 3kdd Chain A Binding Site BS01