Structure of PDB 3mdb Chain C Binding Site BS02

Receptor Information
>3mdb Chain C (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHSSGRENLYFQGMAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLG
VFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFES
KVPSFYYRPTPSDCQLLREQWIRAKYERQEFIYPEKQEPYSAGYREGFLW
KRGRDNGQFLSRKFVLTEREGALKYFNAKEPKAVMKIEHLNATFQPAKIG
HPHGLQVTYLKDNSTRNIFIYHEDGKEIVDWFNALRAARFHYLQVAFPGA
SDADLVPKLSRNYLKEGYMEKFRKRWFTMDDRRLMYFKDPLDAFARGEVF
IGSKESGYTVLHGFPWPHGITIVTPDRKFLFACETESDQREWVAAFQKAV
DRPMLPQEYAVEAHF
Ligand information
Ligand IDIP9
InChIInChI=1S/C25H50O22P4/c1-3-5-7-9-11-13-18(26)41-15-17(43-19(27)14-12-10-8-6-4-2)16-42-51(39,40)47-22-20(28)23(44-48(30,31)32)25(46-50(36,37)38)24(21(22)29)45-49(33,34)35/h17,20-25,28-29H,3-16H2,1-2H3,(H,39,40)(H2,30,31,32)(H2,33,34,35)(H2,36,37,38)/t17-,20+,21+,22-,23+,24-,25-/m1/s1
InChIKeyANFYVAHJWGJYAT-QLCNXWICSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCCCCC(=O)OCC(COP(=O)(O)OC1C(C(C(C(C1O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O)OC(=O)CCCCCCC
CACTVS 3.370CCCCCCCC(=O)OC[CH](CO[P](O)(=O)O[CH]1[CH](O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O)OC(=O)CCCCCCC
OpenEye OEToolkits 1.7.0CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC1[C@@H]([C@H](C([C@H]([C@H]1O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O)OC(=O)CCCCCCC
CACTVS 3.370CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)O[C@@H]1[C@H](O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O)OC(=O)CCCCCCC
ACDLabs 12.01O=C(OCC(OC(=O)CCCCCCC)COP(=O)(O)OC1C(O)C(OP(=O)(O)O)C(OP(=O)(O)O)C(OP(=O)(O)O)C1O)CCCCCCC
FormulaC25 H50 O22 P4
Name(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate;
L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl;
[(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate
ChEMBLCHEMBL1233642
DrugBank
ZINCZINC000097949355
PDB chain3mdb Chain C Residue 375 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3mdb Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4
Resolution2.952 Å
Binding residue
(original residue number in PDB)		K138 G140 R141 R149 Y162 N164 K172 R206
Binding residue
(residue number reindexed from 1)		K151 G153 R154 R162 Y175 N177 K182 R216
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding
GO:0043533 inositol 1,3,4,5 tetrakisphosphate binding
GO:0046872 metal ion binding
GO:1902936 phosphatidylinositol bisphosphate binding
Biological Process
GO:0007166 cell surface receptor signaling pathway
GO:0043087 regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3mdb, PDBe:3mdb, PDBj:3mdb
PDBsum3mdb
PubMed
UniProtO75689|ADAP1_HUMAN Arf-GAP with dual PH domain-containing protein 1 (Gene Name=ADAP1)

[Back to BioLiP]