Structure of PDB 2nva Chain A Binding Site BS02

Receptor Information
>2nva Chain A (length=369) Species: 10506 (Paramecium bursaria Chlorella virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNSVVNNILKAHPHQTKSFYVSSPKIVEDLIDQWTILFPRVTPHYAVKCN
NDEVLLKTMCDKNVNFDCASSSEIKKVIQIGVSPSRIIFAHTMKTIDDLI
FAKDQGVDIATFDSSFELDKIHTYHPNCKMILRIRCDDPNATVQLGNKFG
ANEDEIRHLLEYAKQLDIEVIGISFHVGSGSRNPEAYYRAIKSSKEAFNE
AISVGHKPYILDIGGGLHADIDLSTYMSDYINDAIKDFFPEDTVTIVAEP
GRFFAEHYSVLATQVIGKRVRDGLYEYFFNESTYGGFSNVIFEKSVPTPQ
LLRDVPDDEEYVPSVLYGCTCDGVDVINHNVALPELHIGDWVYFPSWGAY
TNVLTTSFNGFGEYDVYYI
Ligand information
Ligand IDPL2
InChIInChI=1S/C13H24N5O5P/c1-9-12(19)11(7-16-4-2-3-5-17-13(14)15)10(6-18-9)8-23-24(20,21)22/h6,16,19H,2-5,7-8H2,1H3,(H4,14,15,17)(H2,20,21,22)
InChIKeySIKJBFNFPRPKQR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]/N=C(/N)\NCCCCNCc1c(cnc(c1O)C)COP(=O)(O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNCCCCNC(N)=N)c1O
OpenEye OEToolkits 1.5.0[H]N=C(N)NCCCCNCc1c(cnc(c1O)C)COP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNCCCCNC(=[N@H])N)C
FormulaC13 H24 N5 O5 P
Name(4-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000016052261
PDB chain2nva Chain B Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2nva X-ray Structure of Paramecium bursaria Chlorella Virus Arginine Decarboxylase: Insight into the Structural Basis for Substrate Specificity.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		C324 D325
Binding residue
(residue number reindexed from 1)		C321 D322
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K48 H176 E252
Catalytic site (residue number reindexed from 1) K48 H176 E249
Enzyme Commision number 4.1.1.19: arginine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004586 ornithine decarboxylase activity
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0033387 putrescine biosynthetic process from ornithine
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2nva, PDBe:2nva, PDBj:2nva
PDBsum2nva
PubMed17305368
UniProtQ84527

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