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BioLiP

Structure of PDB 2gvv Chain A Binding Site BS03

Receptor Information
>2gvv Chain A (length=309) Species: 6622 (Loligo vulgaris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPVIEPLFTKVTEDIPGAEGPVFDKNGDFYIVAPEVEVNGKPAGEILRID
LKTGKKTVICKPEVNGYGGIPAGCQCDRDANQLFVADMRLGLLVVQTDGT
FEEIAKKDSEGRRMQGCNDCAFDYEGNLWITAPAGEVAPADYTRSMQEKF
GSIYCFTTDGQMIQVDTAFQFPNGIAVRHMNDGRPYQLIVAETPTKKLWS
YDIKGPAKIENKKVWGHIPGTHEGGADGMDFDEDNNLLVANWGSSHIEVF
GPDGGQPKMRIRCPFEKPSNLHFKPQTKTIFVTEHENNAVWKFEWQRNGK
KQYCETLKF
Ligand information
Ligand IDDI9
InChIInChI=1S/C10H20NO3P/c11-15(12,13-9-5-1-2-6-9)14-10-7-3-4-8-10/h9-10H,1-8H2,(H2,11,12)
InChIKeyBDYGAPLPLXNVSE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CCC(C1)OP(=O)(N)OC2CCCC2
CACTVS 3.341N[P](=O)(OC1CCCC1)OC2CCCC2
ACDLabs 10.04O=P(OC1CCCC1)(OC2CCCC2)N
FormulaC10 H20 N O3 P
NameDICYCLOPENTYL PHOSPHORAMIDATE
ChEMBL
DrugBank
ZINCZINC000016052087
PDB chain2gvv Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2gvv Binding of a designed substrate analogue to diisopropyl fluorophosphatase: implications for the phosphotriesterase mechanism.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		E21 P36 N120 N175 D229 W244
Binding residue
(residue number reindexed from 1)		E19 P34 N118 N173 D227 W242
Annotation score1
Binding affinityMOAD: Kd=400uM
PDBbind-CN: -logKd/Ki=3.90,Ki=125uM
Enzymatic activity
Catalytic site (original residue number in PDB) E21 E37 N120 N175 D229 H287
Catalytic site (residue number reindexed from 1) E19 E35 N118 N173 D227 H285
Enzyme Commision number 3.8.2.2: diisopropyl-fluorophosphatase.
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047862 diisopropyl-fluorophosphatase activity
Biological Process
GO:0008150 biological_process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2gvv, PDBe:2gvv, PDBj:2gvv
PDBsum2gvv
PubMed17002369
UniProtQ7SIG4|DFPA_LOLVU Diisopropyl-fluorophosphatase

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