Structure of PDB 5d3y Chain A Binding Site BS01

Receptor Information

>5d3y Chain A (length=136) Species: 9606 (Homo sapiens)

ALEQLQSHIEGWEGSNLTDICTQLLLQGTLLKISAGNIQERAFFLFDNLL
VYCKRKSRVSLYIFRGRINTEVMEVENVEDGTADYHSNGYTVTNGWKIHN
TAKNKWFVCMAKTAEEKQKWLDAIIREREQRESLKL

Ligand information

• Ligand ID: 4IP
• InChI: InChI=1S/C6H16O18P4/c7-1-3(21-25(9,10)11)2(8)5(23-27(15,16)17)6(24-28(18,19)20)4(1)22-26(12,13)14/h1-8H,(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)(H2,18,19,20)/t1-,2-,3-,4+,5-,6-/m0/s1
• InChIKey: CIPFCGZLFXVXBG-CNWJWELYSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OC1C(O)C(OP(=O)(O)O)C(O)C(OP(=O)(O)O)C1OP(=O)(O)O
  OpenEye OEToolkits 1.7.6: [C@H]1([C@H](C([C@H]([C@H](C1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O
  CACTVS 3.385: O[CH]1[CH](O[P](O)(O)=O)[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
  OpenEye OEToolkits 1.7.6: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)O
  CACTVS 3.385: O[C@H]1[C@@H](O[P](O)(O)=O)[C@H](O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
• Formula: C6 H16 O18 P4
• Name: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
• ChEMBL: CHEMBL23552
• DrugBank: DB01863
• ZINC: ZINC000012494830
• PDB chain: 5d3y Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d3y Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): K280 S282 N285 Q287 R289 Y300 R328 K366 K368
• Binding residue (residue number reindexed from 1): K32 S34 N37 Q39 R41 Y52 R65 K103 K105
• Annotation score: 4
• Binding affinity: MOAD: Kd=440nM

External links

• PDB: RCSB:5d3y, PDBe:5d3y, PDBj:5d3y
• PDBsum: 5d3y
• PubMed: 27150042
• UniProt: Q8TCU6|PREX1_HUMAN Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein (Gene Name=PREX1)