Structure of PDB 5th5 Chain D Binding Site BS02

Receptor Information
>5th5 Chain D (length=241) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGIPVLEIFGPTIQGEGMVIGQKTMFVRTAGCDYSCSWCDSAFTWDGSAK
KDIRWMTAEEIFAELKDIGGDAFSHVTISGGNPALLKQLDAFIELLKENN
IRAALETQGTVYQDWFTLIDDLTISPKPPSSKMVTNFQKLDHILTSLQEN
DRQHAVSLKVVIFNDEDLEFAKTVHKRYPGIPFYLQVGNDDVHTTDDQSL
IAHLLGKYEALVDKVAVDAELNLVRVLPQLHTLLWGNKRGV
Ligand information
Ligand ID7C5
InChIInChI=1S/C17H16N10O6/c18-11-7-13(22-3-21-11)27(4-23-7)15-10(29)9(28)6(33-15)2-32-16(31)5-1-20-12-8(24-5)14(30)26-17(19)25-12/h1,3-4,6,9-10,15,28-29H,2H2,(H2,18,21,22)(H3,19,20,25,26,30)/t6-,9-,10-,15-/m1/s1
InChIKeyINIBCQZJBGQGDM-NCEGKOTBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01NC=4Nc5ncc(C(OCC3C(O)C(C(n2cnc1c2ncnc1N)O3)O)=O)nc5C(N=4)=O
OpenEye OEToolkits 2.0.6c1c(nc2c(n1)NC(=NC2=O)N)C(=O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O
CACTVS 3.385NC1=NC(=O)c2nc(cnc2N1)C(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45
CACTVS 3.385NC1=NC(=O)c2nc(cnc2N1)C(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
OpenEye OEToolkits 2.0.6c1c(nc2c(n1)NC(=NC2=O)N)C(=O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
FormulaC17 H16 N10 O6
Name5'-O-(2-amino-4-oxo-1,4-dihydropteridine-6-carbonyl)adenosine
ChEMBL
DrugBank
ZINCZINC000584905389
PDB chain5th5 Chain D Residue 302 [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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PDB5th5 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies.
Resolution2.407 Å
Binding residue
(original residue number in PDB)		I15 Q16 E18 F28 R30 W40 D42 S127 K161 V163 Q188 N191 Q231 H233 V243
Binding residue
(residue number reindexed from 1)		I13 Q14 E16 F26 R28 W38 D40 S125 K159 V161 Q186 N189 Q229 H231 V241
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F28 C34 C41 D42 S43 E108
Catalytic site (residue number reindexed from 1) F26 C32 C39 D40 S41 E106
Enzyme Commision number 4.3.99.3: 7-carboxy-7-deazaguanine synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016840 carbon-nitrogen lyase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0008616 queuosine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5th5, PDBe:5th5, PDBj:5th5
PDBsum5th5
PubMed28045519
UniProtO31677|QUEE_BACSU 7-carboxy-7-deazaguanine synthase (Gene Name=queE)

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