Structure of PDB 4ydg Chain A Binding Site BS01

Receptor Information

>4ydg Chain A (length=108) Species: 11926 (Human T-cell lymphotrophic virus type 1 (strain ATK))

PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTP
LKNTTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQ
CQGVLYLP

Ligand information

• Ligand ID: G3G
• InChI: InChI=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
• InChIKey: XDDOZTWMJWWMBF-KYJUHHDHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CN([C@H]2CNC[C@@H]2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)N)S(=O)(=O)c5ccc(cc5)N
  CACTVS 3.341: Nc1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[C@H]3CNC[C@@H]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(N)cc5
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CN(C2CNCC2N(Cc3ccccc3)S(=O)(=O)c4ccc(cc4)N)S(=O)(=O)c5ccc(cc5)N
  ACDLabs 10.04: O=S(=O)(N(C3C(N(Cc1ccccc1)S(=O)(=O)c2ccc(N)cc2)CNC3)Cc4ccccc4)c5ccc(N)cc5
  CACTVS 3.341: Nc1ccc(cc1)[S](=O)(=O)N(Cc2ccccc2)[CH]3CNC[CH]3N(Cc4ccccc4)[S](=O)(=O)c5ccc(N)cc5
• Formula: C30 H33 N5 O4 S2
• Name: N,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE)
• ChEMBL: CHEMBL1196641
• ZINC: ZINC000016052403
• PDB chain: 4ydg Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ydg Privileged Structures Meet Human T-Cell Leukemia Virus-1 (HTLV-1): C2-Symmetric 3,4-Disubstituted Pyrrolidines as Nonpeptidic HTLV-1 Protease Inhibitors.
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): D32 W98
• Binding residue (residue number reindexed from 1): D32 W90
• Annotation score: 1
• Binding affinity: PDBbind-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

External links

• PDB: RCSB:4ydg, PDBe:4ydg, PDBj:4ydg
• PDBsum: 4ydg
• PubMed: 26000468
• UniProt: P03362|POL_HTL1A Gag-Pro-Pol polyprotein (Gene Name=gag-pro-pol)