Structure of PDB 1dif Chain A Binding Site BS01

Receptor Information
>1dif 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]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDA85
InChIInChI=1S/C44H56F2N8O6/c1-29(2)37(51-41(57)53(5)27-33-21-13-15-23-47-33)39(55)49-35(25-31-17-9-7-10-18-31)43(45,46)44(59,60)36(26-32-19-11-8-12-20-32)50-40(56)38(30(3)4)52-42(58)54(6)28-34-22-14-16-24-48-34/h7-24,29-30,35-38,59-60H,25-28H2,1-6H3,(H,49,55)(H,50,56)(H,51,57)(H,52,58)/t35-,36-,37-,38-/m0/s1
InChIKeyCGJKKYBHEOTRNM-ZQWQDMLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)NC(Cc1ccccc1)C(C(C(Cc2ccccc2)NC(=O)C(C(C)C)NC(=O)N(C)Cc3ccccn3)(F)F)(O)O)NC(=O)N(C)Cc4ccccn4
CACTVS 3.341CC(C)[C@H](NC(=O)N(C)Cc1ccccn1)C(=O)N[C@@H](Cc2ccccc2)C(O)(O)C(F)(F)[C@H](Cc3ccccc3)NC(=O)[C@@H](NC(=O)N(C)Cc4ccccn4)C(C)C
ACDLabs 10.04O=C(N(Cc1ncccc1)C)NC(C(=O)NC(Cc2ccccc2)C(F)(F)C(O)(O)C(NC(=O)C(NC(=O)N(C)Cc3ncccc3)C(C)C)Cc4ccccc4)C(C)C
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)C(C([C@H](Cc2ccccc2)NC(=O)[C@H](C(C)C)NC(=O)N(C)Cc3ccccn3)(F)F)(O)O)NC(=O)N(C)Cc4ccccn4
CACTVS 3.341CC(C)[CH](NC(=O)N(C)Cc1ccccn1)C(=O)N[CH](Cc2ccccc2)C(O)(O)C(F)(F)[CH](Cc3ccccc3)NC(=O)[CH](NC(=O)N(C)Cc4ccccn4)C(C)C
FormulaC44 H56 F2 N8 O6
NameN-{1-BENZYL-2,2-DIFLUORO-3,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE
ChEMBL
DrugBank
ZINCZINC000098208636
PDB chain1dif Chain B Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dif Inhibition and catalytic mechanism of HIV-1 aspartic protease.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R8 D25 G27 A28 D29 G48 G49 V82 I84
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 G48 G49 V82 I84
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.66,Ki=22pM
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
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Biological Process
External links
PDB RCSB:1dif, PDBe:1dif, PDBj:1dif
PDBsum1dif
PubMed8551523
UniProtP03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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