Structure of PDB 3fd6 Chain A Binding Site BS01

Receptor Information
>3fd6 Chain A (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLMPRLGIGMDTC
VIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDN
MLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIV
LGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLVVTQED
VELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQ
RNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQ
AARFCAEIKSPEGHQAWIIGIVEKGNRTARIIDKPRIIEVAP
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3fd6 Chain A Residue 393 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3fd6 Crystal structures of catalytic intermediates of human selenophosphate synthetase 1.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		K32 L38 L42 I66 G67 M68 D69 D110
Binding residue
(residue number reindexed from 1)		K26 L32 L36 I45 G46 M47 D48 D89
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.9.3: selenide, water dikinase.
Gene Ontology
Molecular Function
GO:0004756 selenide, water dikinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0016260 selenocysteine biosynthetic process
GO:0016310 phosphorylation
GO:0036211 protein modification process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0031965 nuclear membrane

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3fd6, PDBe:3fd6, PDBj:3fd6
PDBsum3fd6
PubMed19477186
UniProtP49903|SPS1_HUMAN Selenide, water dikinase 1 (Gene Name=SEPHS1)

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