Structure of PDB 2jaj Chain B Binding Site BS01

Receptor Information
>2jaj Chain B (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLGMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKEVDVARAERQHQ
LYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSR
RKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQ
RGAEILADTFKDYAVSTVPVLHLKSFCSMAGPNLIAIGSSESAQKALKIM
QQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEK
LKDHMLIPVSMSELEKVDGLLTCCSVLINKK
Ligand information
Ligand IDD20
InChIInChI=1S/C9H20N4O3/c1-16-6-5-13-9(11)12-4-2-3-7(10)8(14)15/h7H,2-6,10H2,1H3,(H,14,15)(H3,11,12,13)/t7-/m0/s1
InChIKeyXMBSMMCPKFDGEO-ZETCQYMHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COCCNC(=N)NCCC[C@@H](C(=O)O)N
ACDLabs 10.04O=C(O)C(N)CCCNC(=[N@H])NCCOC
CACTVS 3.341COCCNC(=N)NCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.5.0COCCNC(=N)NCCCC(C(=O)O)N
CACTVS 3.341COCCNC(=N)NCCC[C@H](N)C(O)=O
FormulaC9 H20 N4 O3
NameN~5~-{IMINO[(2-METHOXYETHYL)AMINO]METHYL}-L-ORNITHINE
ChEMBLCHEMBL366222
DrugBank
ZINCZINC000013647968
PDB chain2jaj Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2jaj Disruption of methylarginine metabolism impairs vascular homeostasis.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L29 D72 F75 D78 H172 K174 V267 D268 C273
Binding residue
(residue number reindexed from 1)		L34 D75 F78 D81 H172 K174 V267 D268 C273
Annotation score2
Binding affinityMOAD: ic50<25uM
BindingDB: Ki=13000nM,IC50=29000nM
Enzymatic activity
Enzyme Commision number 3.5.3.18: dimethylargininase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016403 dimethylargininase activity
GO:0016597 amino acid binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0000052 citrulline metabolic process
GO:0003073 regulation of systemic arterial blood pressure
GO:0006525 arginine metabolic process
GO:0006527 arginine catabolic process
GO:0007263 nitric oxide mediated signal transduction
GO:0008285 negative regulation of cell population proliferation
GO:0043116 negative regulation of vascular permeability
GO:0045429 positive regulation of nitric oxide biosynthetic process
GO:0045766 positive regulation of angiogenesis
GO:0046209 nitric oxide metabolic process
GO:1900038 negative regulation of cellular response to hypoxia
Cellular Component
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2jaj, PDBe:2jaj, PDBj:2jaj
PDBsum2jaj
PubMed17273169
UniProtO94760|DDAH1_HUMAN N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (Gene Name=DDAH1)

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