Structure of PDB 1d4l Chain A Binding Site BS01

Receptor Information
>1d4l Chain A (length=99) Species: 11685 (HIV-1 M:B_ARV2/SF2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
Ligand information
Ligand IDPI9
InChIInChI=1S/C32H48N4O6S/c1-22(2)17-18-36(43(40,41)27-15-11-25(33)12-16-27)21-29(37)28-20-24-9-13-26(14-10-24)42-19-7-5-6-8-30(38)35-31(23(3)4)32(39)34-28/h9-16,22-23,28-29,31,37H,5-8,17-21,33H2,1-4H3,(H,34,39)(H,35,38)/t28-,29+,31-/m0/s1
InChIKeyFBNSKSOTNMECSA-FLBADVGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)CCN(C[C@@H](O)[C@@H]1Cc2ccc(OCCCCCC(=O)N[C@@H](C(C)C)C(=O)N1)cc2)[S](=O)(=O)c3ccc(N)cc3
CACTVS 3.341CC(C)CCN(C[CH](O)[CH]1Cc2ccc(OCCCCCC(=O)N[CH](C(C)C)C(=O)N1)cc2)[S](=O)(=O)c3ccc(N)cc3
OpenEye OEToolkits 1.5.0CC(C)CC[N@@](C[C@H]([C@@H]1Cc2ccc(cc2)OCCCCCC(=O)N[C@H](C(=O)N1)C(C)C)O)S(=O)(=O)c3ccc(cc3)N
ACDLabs 10.04O=S(=O)(c1ccc(N)cc1)N(CCC(C)C)CC(O)C3NC(=O)C(NC(=O)CCCCCOc2ccc(cc2)C3)C(C)C
OpenEye OEToolkits 1.5.0CC(C)CCN(CC(C1Cc2ccc(cc2)OCCCCCC(=O)NC(C(=O)N1)C(C)C)O)S(=O)(=O)c3ccc(cc3)N
FormulaC32 H48 N4 O6 S
Name(10S,13S,1'R)-13-[1'-HYDROXY-2'-(N-P-AMINOBENZENESULFONYL-1''-AMINO-3''-METHYLBUTYL)ETHYL]-8,11-DIOXO-10-ISOPROPYL-2-OXA-9,12-DIAZABICYCLO [13.2.2]NONADECA-15,17,18-TRIENE
ChEMBLCHEMBL442738
DrugBank
ZINCZINC000029399681
PDB chain1d4l Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1d4l Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		D25 G27 A28 D29 G48 I50 V82 I84
Binding residue
(residue number reindexed from 1)		D25 G27 A28 D29 G48 I50 V82 I84
Annotation score1
Binding affinityMOAD: Ki=1.7nM
PDBbind-CN: -logKd/Ki=8.77,Ki=1.7nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1d4l, PDBe:1d4l, PDBj:1d4l
PDBsum1d4l
PubMed11000004
UniProtP03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)

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