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Receptor Information

>2rkf 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]

PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEMSLPGRWTPKVVGGI
GGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF

Ligand ID

AB1

InChI

InChI=1S/C37H48N4O5/c1-25(2)34(41-20-12-19-38-37(41)45)36(44)39-30(21-28-15-7-5-8-16-28)23-32(42)31(22-29-17-9-6-10-18-29)40-33(43)24-46-35-26(3)13-11-14-27(35)4/h5-11,13-18,25,30-32,34,42H,12,19-24H2,1-4H3,(H,38,45)(H,39,44)(H,40,43)/t30-,31-,32-,34-/m0/s1

InChIKey

KJHKTHWMRKYKJE-SUGCFTRWSA-N

SMILES

Software	SMILES
ACDLabs 10.04	O=C(NC(Cc1ccccc1)C(O)CC(NC(=O)C(N2C(=O)NCCC2)C(C)C)Cc3ccccc3)COc4c(cccc4C)C
OpenEye OEToolkits 1.5.0	Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](C[C@H](Cc3ccccc3)NC(=O)[C@H](C(C)C)N4CCCNC4=O)O)C
CACTVS 3.341	CC(C)[C@H](N1CCCNC1=O)C(=O)N[C@H](C[C@H](O)[C@H](Cc2ccccc2)NC(=O)COc3c(C)cccc3C)Cc4ccccc4
CACTVS 3.341	CC(C)[CH](N1CCCNC1=O)C(=O)N[CH](C[CH](O)[CH](Cc2ccccc2)NC(=O)COc3c(C)cccc3C)Cc4ccccc4
OpenEye OEToolkits 1.5.0	Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(CC(Cc3ccccc3)NC(=O)C(C(C)C)N4CCCNC4=O)O)C

Formula

C37 H48 N4 O5

Name

N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE;
ABT-378;
LOPINAVIR

PDB chain

2rkf Chain A Residue 501 [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	2rkf Ninety-nine is not enough: molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region
Resolution	1.8 Å
Binding residue (original residue number in PDB)	D25 G27 A28 D29 I32 G48 G49 A82 I84
Binding residue (residue number reindexed from 1)	D25 G27 A28 D29 I32 G48 G49 A82 I84
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=9.08,Ki=0.83nM

Catalytic site (original residue number in PDB)	D25 T26 G27
Catalytic site (residue number reindexed from 1)	D25 T26 G27
Enzyme Commision number	3.1.26.13: retroviral ribonuclease H.

	Molecular Function
GO:0004190	aspartic-type endopeptidase activity

	Biological Process
GO:0006508	proteolysis

PDB	RCSB:2rkf, PDBe:2rkf, PDBj:2rkf
PDBsum	2rkf
PubMed	18400858
UniProt	Q90JJ9

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Structure of PDB 2rkf Chain B Binding Site BS01