Structure of PDB 4np9 Chain A Binding Site BS01

Receptor Information

>4np9 Chain A (length=128) Species: 10116 (Rattus norvegicus)

TLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGAS
KSNKLRTKTLRNTRNPVWNETLQYHGITEEDMQRKTLRISVCDEDKFGHN
EFIGETRFSLKKLKANQRKNFNICLERV

Ligand information

• Ligand ID: I3P
• InChI: InChI=1S/C6H15O15P3/c7-1-2(8)5(20-23(13,14)15)6(21-24(16,17)18)3(9)4(1)19-22(10,11)12/h1-9H,(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)/t1-,2+,3+,4-,5-,6-/m1/s1
• InChIKey: MMWCIQZXVOZEGG-XJTPDSDZSA-N
• SMILES:
  ACDLabs 10.04: O=P(OC1C(O)C(O)C(OP(=O)(O)O)C(O)C1OP(=O)(O)O)(O)O
  OpenEye OEToolkits 1.5.0: C1(C(C(C(C(C1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O)[CH]1O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: [C@H]1([C@@H]([C@H]([C@@H]([C@H]([C@@H]1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[C@@H]1[C@H](O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O)[C@@H]1O[P](O)(O)=O
• Formula: C6 H15 O15 P3
• Name: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
• ChEMBL: CHEMBL279107
• DrugBank: DB03401
• ZINC: ZINC000004095598
• PDB chain: 4np9 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4np9 Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1.
• Resolution: 1.92 Å
• Binding residue (original residue number in PDB): Y421 K423 K435 R437 N481 V509
• Binding residue (residue number reindexed from 1): Y40 K42 K54 R56 N100 V128
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.03,Kd=9.4uM

Gene Ontology

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:4np9, PDBe:4np9, PDBj:4np9
• PDBsum: 4np9
• PubMed: 24302762
• UniProt: P47709|RP3A_RAT Rabphilin-3A (Gene Name=Rph3a)