Structure of PDB 3pgl Chain A Binding Site BS02

Receptor Information

>3pgl Chain A (length=180) Species: 9606 (Homo sapiens)

QYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQ
VYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARL
FRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWF
DNMSDTELHDLLPFFEQLSRVDDVYSVLRQ

Ligand information

• Ligand ID: RZX
• InChI: InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)/t25-/m1/s1
• InChIKey: YREYEVIYCVEVJK-RUZDIDTESA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: Cc1c(ccnc1C[S@@](=O)c2[nH]c3ccccc3n2)OCCCOC
  CACTVS 3.370: COCCCOc1ccnc(C[S](=O)c2[nH]c3ccccc3n2)c1C
  ACDLabs 12.01: O=S(c2nc1ccccc1n2)Cc3nccc(OCCCOC)c3C
  OpenEye OEToolkits 1.7.0: Cc1c(ccnc1CS(=O)c2[nH]c3ccccc3n2)OCCCOC
  CACTVS 3.370: COCCCOc1ccnc(C[S@@](=O)c2[nH]c3ccccc3n2)c1C
• Formula: C18 H21 N3 O3 S
• Name: 2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole;
  Rabeprazole
• ChEMBL: CHEMBL1615209
• DrugBank: DB13762
• ZINC: ZINC000001530935
• PDB chain: 3pgl Chain A Residue 257

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pgl Selective inactivation of a human neuronal silencing phosphatase by a small molecule inhibitor.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): F106 Y158 R178
• Binding residue (residue number reindexed from 1): F30 Y82 R102
• Annotation score: 1
• Binding affinity: MOAD: Ki=5uM
  PDBbind-CN: -logKd/Ki=5.30,Ki=5uM

Enzymatic activity

• Enzyme Commision number: 3.1.3.16: protein-serine/threonine phosphatase.

Gene Ontology

Molecular Function

• GO:0008420 RNA polymerase II CTD heptapeptide repeat phosphatase activity
• GO:0016791 phosphatase activity

External links

• PDB: RCSB:3pgl, PDBe:3pgl, PDBj:3pgl
• PDBsum: 3pgl
• PubMed: 21348431
• UniProt: Q9GZU7|CTDS1_HUMAN Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (Gene Name=CTDSP1)