Structure of PDB 4ydg Chain B Binding Site BS01

Receptor Information
>4ydg Chain B (length=111) Species: 11926 (Human T-cell lymphotrophic virus type 1 (strain ATK)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTP
LKNTSVLTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDA
LQQCQGVLYLP
Ligand information
Ligand IDG3G
InChIInChI=1S/C30H33N5O4S2/c31-25-11-15-27(16-12-25)40(36,37)34(21-23-7-3-1-4-8-23)29-19-33-20-30(29)35(22-24-9-5-2-6-10-24)41(38,39)28-17-13-26(32)14-18-28/h1-18,29-30,33H,19-22,31-32H2/t29-,30-/m0/s1
InChIKeyXDDOZTWMJWWMBF-KYJUHHDHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN([C@H]2CNC[C@@H]2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)N)S(=O)(=O)c5ccc(cc5)N
CACTVS 3.341Nc1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[C@H]3CNC[C@@H]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(N)cc5
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN(C2CNCC2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)N)S(=O)(=O)c5ccc(cc5)N
ACDLabs 10.04O=S(=O)(N(C3C(N(Cc1ccccc1)S(=O)(=O)c2ccc(N)cc2)CNC3)Cc4ccccc4)c5ccc(N)cc5
CACTVS 3.341Nc1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[CH]3CNC[CH]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(N)cc5
FormulaC30 H33 N5 O4 S2
NameN,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE)
ChEMBLCHEMBL1196641
DrugBank
ZINCZINC000016052403
PDB chain4ydg Chain B Residue 201 [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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PDB4ydg Privileged Structures Meet Human T-Cell Leukemia Virus-1 (HTLV-1): C2-Symmetric 3,4-Disubstituted Pyrrolidines as Nonpeptidic HTLV-1 Protease Inhibitors.
Resolution3.25 Å
Binding residue
(original residue number in PDB)		D32 G34 A35 D36 M37 W98
Binding residue
(residue number reindexed from 1)		D32 G34 A35 D36 M37 W93
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.82,Ki=0.015uM
Enzymatic activity
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.26.4: ribonuclease H.
3.4.23.-
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:4ydg, PDBe:4ydg, PDBj:4ydg
PDBsum4ydg
PubMed26000468
UniProtP03362|POL_HTL1A Gag-Pro-Pol polyprotein (Gene Name=gag-pro-pol)

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