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Structure of PDB 1d4j Chain B Binding Site BS01

Receptor Information
>1d4j Chain B (length=99) Species: 12721 (Human immunodeficiency virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand IDMSC
InChIInChI=1S/C36H36ClFN2O7/c37-27-16-9-17-28(38)26(27)19-39-35(44)33(46-20-22-10-3-1-4-11-22)31(42)32(43)34(47-21-23-12-5-2-6-13-23)36(45)40-30-25-15-8-7-14-24(25)18-29(30)41/h1-17,29-34,41-43H,18-21H2,(H,39,44)(H,40,45)/t29-,30+,31-,32-,33-,34-/m1/s1
InChIKeyBVPTXJDSYPTXMO-VQEIZDKSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Fc1cccc(Cl)c1CNC(=O)C(OCc2ccccc2)C(O)C(O)C(OCc3ccccc3)C(=O)NC5c4ccccc4CC5O
CACTVS 3.341O[C@@H]1Cc2ccccc2[C@@H]1NC(=O)[C@H](OCc3ccccc3)[C@H](O)[C@@H](O)[C@@H](OCc4ccccc4)C(=O)NCc5c(F)cccc5Cl
OpenEye OEToolkits 1.5.0c1ccc(cc1)CO[C@H]([C@@H]([C@H]([C@H](C(=O)N[C@H]2c3ccccc3C[C@H]2O)OCc4ccccc4)O)O)C(=O)NCc5c(cccc5Cl)F
CACTVS 3.341O[CH]1Cc2ccccc2[CH]1NC(=O)[CH](OCc3ccccc3)[CH](O)[CH](O)[CH](OCc4ccccc4)C(=O)NCc5c(F)cccc5Cl
OpenEye OEToolkits 1.5.0c1ccc(cc1)COC(C(C(C(C(=O)NC2c3ccccc3CC2O)OCc4ccccc4)O)O)C(=O)NCc5c(cccc5Cl)F
FormulaC36 H36 Cl F N2 O7
Name2,5-DIBENZYLOXY-3,4-DIHYDROXY-HEXANEDIOIC ACID 2-CHLORO-6-FLUORO-BENZYLAMIDE (2-HYDROXY-INDAN-1- YL)-AMIDE;
INHIBITOR MSL370
ChEMBL
DrugBank
ZINCZINC000024465991
PDB chain1d4j Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1d4j Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors.
Resolution1.81 Å
Binding residue
(original residue number in PDB)		R108 D125 G127 A128 D129 D130 I147 G148 P181 V182
Binding residue
(residue number reindexed from 1)		R8 D25 G27 A28 D29 D30 I47 G48 P81 V82
Annotation score1
Binding affinityMOAD: Ki=4.4nM
PDBbind-CN: -logKd/Ki=8.36,Ki=4.40nM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
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:1d4j, PDBe:1d4j, PDBj:1d4j
PDBsum1d4j
PubMed12694187
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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