Structure of PDB 4xpj Chain A Binding Site BS01

Receptor Information

>4xpj Chain A (length=105) Species: 10090 (Mus musculus)

GEFSVCDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCR
ASNPVESGCRGIDSKHWNSYCTTTHTFVKALTTDEKQAAWRFIRIDTACV
CVLSR

Ligand information

• Ligand ID: LPY
• InChI: InChI=1S/C22H43O12P/c1-2-3-4-5-6-7-8-9-10-11-12-16(24)32-13-15(23)14-33-35(30,31)34-22-20(28)18(26)17(25)19(27)21(22)29/h15,17-23,25-29H,2-14H2,1H3,(H,30,31)/t15-,17-,18-,19+,20-,21-,22-/m1/s1
• InChIKey: QGSQXOJTKFYHRK-FBYKMOGESA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)O)O)O)O)O
  CACTVS 3.385: CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P](O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O
  OpenEye OEToolkits 1.9.2: CCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@H]([C@H](C([C@H]([C@H]1O)O)O)O)O)O
  CACTVS 3.385: CCCCCCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)O[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 12.01: P(OC1C(O)C(O)C(O)C(O)C1O)(O)(=O)OCC(O)COC(=O)CCCCCCCCCCCC
• Formula: C22 H43 O12 P
• Name: (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate;
  sn-1-tridecanoyl-phosphatidylinositol
• ZINC: ZINC000263620935
• PDB chain: 4xpj Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4xpj The structure of nerve growth factor in complex with lysophosphatidylinositol
• Resolution: 2.605 Å
• Binding residue (original residue number in PDB): K88 W99
• Binding residue (residue number reindexed from 1): K79 W90
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.09,Kd~8.11uM

Gene Ontology

Molecular Function

• GO:0005102 signaling receptor binding

External links

• PDB: RCSB:4xpj, PDBe:4xpj, PDBj:4xpj
• PDBsum: 4xpj
• PubMed: 26144237
• UniProt: P01139|NGF_MOUSE Beta-nerve growth factor (Gene Name=Ngf)