Structure of PDB 6cdj Chain A Binding Site BS01

Receptor Information
>6cdj Chain A (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]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDGR8
InChIInChI=1S/C34H42F2N4O7S2/c1-18(2)15-40(49(43,44)24-5-6-26-30(14-24)48-33(38-26)37-23-3-4-23)16-28(41)27(11-19-9-21(35)13-22(36)10-19)39-34(42)47-29-12-20-17-46-32-31(20)25(29)7-8-45-32/h5-6,9-10,13-14,18,20,23,25,27-29,31-32,41H,3-4,7-8,11-12,15-17H2,1-2H3,(H,37,38)(H,39,42)/t20-,25-,27+,28-,29-,31+,32+/m1/s1
InChIKeyNIZKZMLJMFCQSW-FQOBIZQLSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01s1c3c(nc1NC2CC2)ccc(c3)S(=O)(=O)N(CC(C(Cc4cc(F)cc(c4)F)NC(=O)OC5CC7C6C5CCOC6OC7)O)CC(C)C
OpenEye OEToolkits 2.0.6CC(C)CN(C[C@H]([C@H](Cc1cc(cc(c1)F)F)NC(=O)O[C@@H]2C[C@@H]3CO[C@H]4[C@@H]3[C@@H]2CCO4)O)S(=O)(=O)c5ccc6c(c5)sc(n6)NC7CC7
OpenEye OEToolkits 2.0.6CC(C)CN(CC(C(Cc1cc(cc(c1)F)F)NC(=O)OC2CC3COC4C3C2CCO4)O)S(=O)(=O)c5ccc6c(c5)sc(n6)NC7CC7
CACTVS 3.385CC(C)CN(C[C@@H](O)[C@H](Cc1cc(F)cc(F)c1)NC(=O)O[C@@H]2C[C@@H]3CO[C@@H]4OCC[C@H]2[C@H]34)[S](=O)(=O)c5ccc6nc(NC7CC7)sc6c5
CACTVS 3.385CC(C)CN(C[CH](O)[CH](Cc1cc(F)cc(F)c1)NC(=O)O[CH]2C[CH]3CO[CH]4OCC[CH]2[CH]34)[S](=O)(=O)c5ccc6nc(NC7CC7)sc6c5
FormulaC34 H42 F2 N4 O7 S2
Name
ChEMBLCHEMBL4214453
DrugBank
ZINC
PDB chain6cdj 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]
PDB6cdj Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis.
Resolution1.13 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 D30 G48 G49 I50
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 D30 G48 G49 I50
Annotation score1
Binding affinityMOAD: Ki=2pM
PDBbind-CN: -logKd/Ki=11.70,Ki=0.002nM
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 ?
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:6cdj, PDBe:6cdj, PDBj:6cdj
PDBsum6cdj
PubMed29763303
UniProtQ5RZ08

[Back to BioLiP]