Structure of PDB 3p8p Chain A Binding Site BS01

Receptor Information
>3p8p Chain A (length=275) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSK
LGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKE
ALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADT
FKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDH
RYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHML
IPVSMSELEKVDGLLTSCSVLINKK
Ligand information
Ligand IDLN6
InChIInChI=1S/C10H21N3O2/c1-2-3-6-9(12)13-7-4-5-8(11)10(14)15/h8H,2-7,11H2,1H3,(H2,12,13)(H,14,15)/t8-/m0/s1
InChIKeyYJYNJYPKPDAGPU-QMMMGPOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCC(=N)NCCC[C@H](N)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCNC(=[N@H])CCCC
CACTVS 3.370CCCCC(=N)NCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.7.0CCCCC(=N)NCCCC(C(=O)O)N
OpenEye OEToolkits 1.7.0[H]/N=C(\CCCC)/NCCC[C@@H](C(=O)O)N
FormulaC10 H21 N3 O2
NameN~5~-[(1E)-pentanimidoyl]-L-ornithine;
N5-(1-iminopentyl)-L-ornithine
ChEMBL
DrugBank
ZINCZINC000038812736
PDB chain3p8p Chain A Residue 286 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3p8p Characterization of C-Alkyl Amidines as Bioavailable Covalent Reversible Inhibitors of Human DDAH-1.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L30 D73 F76 D79 R98 R145 H173 K175 V268 D269 S274
Binding residue
(residue number reindexed from 1)		L23 D66 F69 D72 R91 R138 H166 K168 V261 D262 S267
Annotation score3
Binding affinityMOAD: Kd=28uM
PDBbind-CN: -logKd/Ki=4.55,Kd=28uM
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
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Cellular Component
External links
PDB RCSB:3p8p, PDBe:3p8p, PDBj:3p8p
PDBsum3p8p
PubMed20979083
UniProtO94760|DDAH1_HUMAN N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (Gene Name=DDAH1)

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