Structure of PDB 3hii Chain B Binding Site BS04

Receptor Information
>3hii Chain B (length=710) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKAGVFSDLSNQELKAVHSFLWSKKELRLQPSSTTTMAKNTVFLIEMLLP
KKYHVLRFLDKGERHPVREARAVIFFGDQEHPNVTEFAVGPLPGPCYMRA
LSPRPGYQSSWASRPISTAEYALLYHTLQEATKPLHQFFLNTTGFSFQDC
HDRCLAFTDVAPRGVASGQRRSWLIIQRYVEGYFLHPTGLELLVDHGSTD
AGHWAVEQVWYNGKFYGSPEELARKYADGEVDVVVLEPPLFSSHKPRGDF
PSPIHVSGPRLVQPHGPRFRLEGNAVLYGGWSFAFRLRSSSGLQVLNVHF
GGERIAYEVSVQEAVALYGGHTPAGMQTKYLDVGWGLGSVTHELAPGIDC
PETATFLDTFHYYDADDPVHYPRALCLFEMPTGVPLRRHFNSNFKGGFNF
YAGLKGQVLVLRTTSTVYNYDYIWDFIFYPNGVMEAKMHATGYVHATFYT
PEGLRHGTRLHTHLIGNIHTHLVHYRVDLDVAGTKNSFQTLQMKLENITN
PWSPRHRVVQPTLEQTQYSWERQAAFRFKRKLPKYLLFTSPQENPWGHKR
SYRLQIHSMADQVLPPGWQEEQAITWARYPLAVTKYRESELCSSSIYHQN
DPWDPPVVFEQFLHNNENIENEDLVAWVTVGFLHIPHSEDIPNTATPGNS
VGFLLRPFNFFPEDPSLASRDTVIVWPRDNGPNYVQRWIPEDRDCSMPPP
FSYNGTYRPV
Ligand information
Ligand IDPNT
InChIInChI=1S/C19H24N4O2/c20-18(21)14-4-8-16(9-5-14)24-12-2-1-3-13-25-17-10-6-15(7-11-17)19(22)23/h4-11H,1-3,12-13H2,(H3,20,21)(H3,22,23)
InChIKeyXDRYMKDFEDOLFX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O(c1ccc(cc1)C(=[N@H])N)CCCCCOc2ccc(C(=[N@H])N)cc2
CACTVS 3.341NC(=N)c1ccc(OCCCCCOc2ccc(cc2)C(N)=N)cc1
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=N)N)OCCCCCOc2ccc(cc2)C(=N)N
FormulaC19 H24 N4 O2
Name1,5-BIS(4-AMIDINOPHENOXY)PENTANE
ChEMBLCHEMBL55
DrugBankDB00738
ZINCZINC000001530775
PDB chain3hii Chain B Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3hii Structure and inhibition of human diamine oxidase
Resolution2.149 Å
Binding residue
(original residue number in PDB)		Y148 D186 Y371 D373 W376 G377 V381 Y404 Y459 N460
Binding residue
(residue number reindexed from 1)		Y121 D159 Y330 D332 W335 G336 V340 Y363 Y418 N419
Annotation score1
Binding affinityMOAD: Ki=290nM
PDBbind-CN: -logKd/Ki=6.54,Ki=290nM
BindingDB: Ki=290nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y359 D373 Y461 H510 H512 H675
Catalytic site (residue number reindexed from 1) Y318 D332 Y420 H469 H471 H634
Enzyme Commision number 1.4.3.22: diamine oxidase.
Gene Ontology
Molecular Function
GO:0005507 copper ion binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008131 primary methylamine oxidase activity
GO:0008201 heparin binding
GO:0016491 oxidoreductase activity
GO:0016641 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0048038 quinone binding
GO:0050232 putrescine oxidase activity
GO:0052597 diamine oxidase activity
GO:0052598 histamine oxidase activity
Biological Process
GO:0009308 amine metabolic process
GO:0009445 putrescine metabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005777 peroxisome
GO:0005886 plasma membrane
GO:0005923 bicellular tight junction
GO:0035580 specific granule lumen
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:3hii, PDBe:3hii, PDBj:3hii
PDBsum3hii
PubMed19764817
UniProtP19801|AOC1_HUMAN Diamine oxidase [copper-containing] (Gene Name=AOC1)

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