Structure of PDB 6szp Chain A Binding Site BS01

Receptor Information
>6szp 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
IPVSMSELEKVDGLLTCCSVLINKK
Ligand information
Ligand IDM3B
InChIInChI=1S/C8H22N4O/c1-13-7-6-12-8(10)11-5-3-2-4-9/h8,11-12H,2-7,9-10H2,1H3/t8-/m0/s1
InChIKeyHBYRDDGQNQMGCZ-QMMMGPOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COCCN[CH](N)NCCCCN
OpenEye OEToolkits 2.0.7COCCNC(N)NCCCCN
CACTVS 3.385
OpenEye OEToolkits 2.0.7		COCCN[C@@H](N)NCCCCN
FormulaC8 H22 N4 O
Name(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine
ChEMBL
DrugBank
ZINC
PDB chain6szp Chain A Residue 300 [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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PDB6szp Discovery ofN-(4-Aminobutyl)-N'-(2-methoxyethyl)guanidine as the First Selective, Nonamino Acid, Catalytic Site Inhibitor of Human Dimethylarginine Dimethylaminohydrolase-1 (hDDAH-1).
Resolution1.76 Å
Binding residue
(original residue number in PDB)		L30 D73 F76 D79 H173 V268 D269 C274
Binding residue
(residue number reindexed from 1)		L23 D66 F69 D72 H166 V261 D262 C267
Annotation score1
Binding affinityMOAD: Ki=18uM
PDBbind-CN: -logKd/Ki=4.74,Ki=18uM
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:6szp, PDBe:6szp, PDBj:6szp
PDBsum6szp
PubMed31841335
UniProtO94760|DDAH1_HUMAN N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (Gene Name=DDAH1)

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