Structure of PDB 3vaf Chain B Binding Site BS03

Receptor Information

>3vaf Chain B (length=172) Species: 9606 (Homo sapiens)

LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD
KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIG
GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD
QAIAGLNGMQLGDKKLLVQRAS

Ligand information

• Ligand ID: CPQ
• InChI: InChI=1S/C42H75N3O15/c1-22(26-9-10-27-25-8-7-23-18-24(48)12-13-41(23,2)28(25)19-31(51)42(26,27)3)6-11-32(52)45(16-4-14-43-39(59)37(57)35(55)33(53)29(49)20-46)17-5-15-44-40(60)38(58)36(56)34(54)30(50)21-47/h22-31,33-38,46-51,53-58H,4-21H2,1-3H3,(H,43,59)(H,44,60)/t22-,23-,24-,25+,26-,27+,28+,29-,30-,31+,33-,34-,35+,36+,37-,38-,41+,42-/m1/s1
• InChIKey: OJSUWTDDXLCUFR-HGZMBBKESA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H](CCC(=O)N(CCCNC(=O)[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O)CCCNC(=O)[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C@H]3[C@H]2CC[C@H]4[C@@]3(CC[C@H](C4)O)C)O)C
  OpenEye OEToolkits 1.5.0: CC(CCC(=O)N(CCCNC(=O)C(C(C(C(CO)O)O)O)O)CCCNC(=O)C(C(C(C(CO)O)O)O)O)C1CCC2C1(C(CC3C2CCC4C3(CCC(C4)O)C)O)C
  ACDLabs 10.04: O=C(NCCCN(C(=O)CCC(C4CCC3C2C(C1(C)CCC(O)CC1CC2)CC(O)C34C)C)CCCNC(=O)C(O)C(O)C(O)C(O)CO)C(O)C(O)C(O)C(O)CO
  CACTVS 3.341: C[C@H](CCC(=O)N(CCCNC(=O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)CCCNC(=O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
  CACTVS 3.341: C[CH](CCC(=O)N(CCCNC(=O)[CH](O)[CH](O)[CH](O)[CH](O)CO)CCCNC(=O)[CH](O)[CH](O)[CH](O)[CH](O)CO)[CH]1CC[CH]2[CH]3CC[CH]4C[CH](O)CC[C]4(C)[CH]3C[CH](O)[C]12C
• Formula: C42 H75 N3 O15
• Name: N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE;
  DEOXY-BIGCHAP
• DrugBank: DB01890
• ZINC: ZINC000169615617
• PDB chain: 3vaf Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vaf U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
• Resolution: 2.49 Å
• Binding residue (original residue number in PDB): Y269 L270 Q274 L325 G326
• Binding residue (residue number reindexed from 1): Y105 L106 Q110 L161 G162
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding

External links

• PDB: RCSB:3vaf, PDBe:3vaf, PDBj:3vaf
• PDBsum: 3vaf
• PubMed: 23376934
• UniProt: P26368|U2AF2_HUMAN Splicing factor U2AF 65 kDa subunit (Gene Name=U2AF2)