Structure of PDB 4gbd Chain B Binding Site BS01

Receptor Information
>4gbd Chain B (length=434) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFDLLLLPTWIVPVEPAGVVLRDHALGIRDGQIALVAPREQAMRHGATEI
RELPGMLLAPGLVNAHGHSAMSLFRGLADDLPLMTWLQDHIWPAEGQWVS
EDFIRDGTELAIAEQVKGGITCFSDMYFYPQAICGVVHDSGVRAQVAIPV
LDFPIPGARDSAEAIRQGMALFDDLKHHPRIRIAFGPHAPYTVSDDKLEQ
ILVLTEELDASIQMHVHETAFEVEQAMERNGERPLARLHRLGLLGPRFQA
VHMTQVDNDDLAMLVETNSSVIHCPESNLKLASGFCPVEKLWQAGVNVAI
GTDGAASNNDLDLLGETRTAALLAKAVYGQATALDAHRALRMATLNGARA
LGLERLIGSLEAGKAADLVAFDLSGLAQQPVYDPVSQLIYASGRDCVRHV
WVGGRQLLDDGRLLRHDEQRLIARAREWGAKIAA
Ligand information
Ligand IDMCF
InChIInChI=1S/C12H18N4O4S/c1-21-3-7-9(18)10(19)12(20-7)16-5-15-8-6(17)2-13-4-14-11(8)16/h4-7,9-10,12,17-19H,2-3H2,1H3,(H,13,14)/t6-,7-,9-,10-,12-/m1/s1
InChIKeyQLPPCUVJNCMYFD-SANHVUMCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2N=CNCC3O)O)O
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2N=CNC[C@H]3O)O)O
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3[CH](O)CNC=Nc23
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3[C@H](O)CNC=Nc23
ACDLabs 10.04n2c1c(N=CNCC1O)n(c2)C3OC(C(O)C3O)CSC
FormulaC12 H18 N4 O4 S
Name(8R)-3-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol
ChEMBLCHEMBL1234234
DrugBank
ZINCZINC000043171427
PDB chain4gbd Chain B Residue 501 [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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PDB4gbd Methylthioadenosine deaminase in an alternative quorum sensing pathway in Pseudomonas aeruginosa.
Resolution1.975 Å
Binding residue
(original residue number in PDB)		H74 M77 L89 W92 W98 E101 M132 Y133 F134 H194 H221 E224 H258 D309
Binding residue
(residue number reindexed from 1)		H68 M71 L83 W86 W92 E95 M126 Y127 F128 H188 H215 E218 H252 D303
Annotation score2
Binding affinityMOAD: Ki=0.0048nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004000 adenosine deaminase activity
GO:0016787 hydrolase activity
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0046872 metal ion binding
GO:0090614 5'-methylthioadenosine deaminase activity

View graph for
Molecular Function
External links
PDB RCSB:4gbd, PDBe:4gbd, PDBj:4gbd
PDBsum4gbd
PubMed23050701
UniProtQ9HZ64

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