Structure of PDB 2cfd Chain B Binding Site BS02

Receptor Information
>2cfd Chain B (length=619) Species: 1665 (Arthrobacter globiformis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASPFRLASAGEISEVQGILRTAGLLGPEKRIAYLGVLDPARGAGSEAEDR
RFRVFIHDVSGARPQEVTVSVTNGTVISAVELDTAATGELPVLEEEFEVV
EQLLATDERWLKALAARNLDVSKVRVAPLSAGVFEYAEERGRRILRGLAF
VQDFPEDSAWAHPVDGLVAYVDVVSKEVTRVIDTGVFPVPAEHGNYTDPE
LTGPLRTTQKPISITQPEGPSFTVTGGNHIEWEKWSLDVGFDVREGVVLH
NIAFRDGDRLRPIINRASIAEMVVPYGDPSPIRSWQNYFDTGEYLVGQYA
NSLELGCDCLGDITYLSPVISDAFGNPREIRNGICMHEEDWGILAKHSDL
WSGINYTRRNRRMVISFFTTIGNYDYGFYWYLYLDGTIEFEAKATGVVFT
SAFPEGGSDNISQLAPGLGAPFHQHIFSARLDMAIDGFTNRVEEEDVVRQ
TMGPGNERGNAFSRKRTVLTRESEAVREADARTGRTWIISNPESKNRLNE
PVGYKLHAHNQPTLLADPGSSIARRAAFATKDLWVTRYADDERYPTGDFV
NQHSGGAGLPSYIAQDRDIDGQDIVVWHTFGLTHFPRVEDWPIMPVDTVG
FKLRPEGFFDRSPVLDVPA
Ligand information
Ligand IDR4A
InChIInChI=1S/C24H27N3O.C10H18N2.C10H16N2.Ru/c1-27(2)20-9-5-10-21(17-20)28-16-4-3-7-18-13-15-26-24-22(18)12-11-19-8-6-14-25-23(19)24;2*1-3-7-11-9(5-1)10-6-2-4-8-12-10;/h5-6,8-14,17,22H,3-4,7,15-16H2,1-2H3;9-10H,1-8H2;1,5,9-10H,2-4,6-8H2;/q3*-2;+6/t;9-,10?;9?,10-;/m.11./s1
InChIKeyLKBNPCYTIAPTEX-RKQPFBAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(C)c1cccc(c1)OCCCCC2=CCN3C4=C5C(=CC=CN5[Ru]367(N8CCCCC8C9N6CCCC9)N1CCCCC1C1N7CCC=C1)C=CC24
CACTVS 3.341CN(C)c1cccc(OCCCCC2=CCN3C4=C5N(C=CC=C5C=C[CH]24)[Ru]367(N8CCCC[CH]8[CH]9CCCCN69)N%10CCCC[CH]%10[CH]%11C=CCCN7%11)c1
ACDLabs 10.04O(c1cccc(N(C)C)c1)CCCCC2=CCN8C3=C4C(C=CC23)=CC=CN4[Ru]86%11(N7C(C5N6CCCC5)CCCC7)N9CCC=CC9C%10N%11CCCC%10
CACTVS 3.341CN(C)c1cccc(OCCCCC2=CCN3C4=C5N(C=CC=C5C=C[C@H]24)[Ru]367(N8CCCC[C@H]8[C@H]9CCCCN69)N%10CCCC[C@@H]%10[C@@H]%11C=CCCN7%11)c1
FormulaC44 H61 N7 O Ru
NameBIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~]{3-[4-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)BUTOXY]-N,N-DIMETHYLANILINATO(2-)}RUTHENIUM
ChEMBL
DrugBank
ZINC
PDB chain2cfd Chain B Residue 705 [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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PDB2cfd Enantiomer-Specific Binding of Ruthenium(II) Molecular Wires by the Amine Oxidase of Arthrobacter Globiformis.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
E102 F105 P136 L137 W168 Y296 Y302 Q306 Y307 R336 T378 G380 A382
Binding residue
(residue number reindexed from 1)
E94 F97 P128 L129 W160 Y288 Y294 Q298 Y299 R328 T370 G372 A374
Annotation score1
Binding affinityMOAD: Ki=32nM
PDBbind-CN: -logKd/Ki=7.49,Ki=32nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y284 D298 Y382 H431 H433 H592
Catalytic site (residue number reindexed from 1) Y276 D290 Y374 H423 H425 H584
Enzyme Commision number 1.4.3.21: primary-amine oxidase.
Gene Ontology
Molecular Function
GO:0005507 copper ion binding
GO:0008131 primary methylamine oxidase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0048038 quinone binding
GO:0052595 aliphatic amine oxidase activity
Biological Process
GO:0009308 amine metabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:2cfd, PDBe:2cfd, PDBj:2cfd
PDBsum2cfd
PubMed18507382
UniProtP46881|PAOX_ARTGO Phenylethylamine oxidase

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