Structure of PDB 7n7c Chain A Binding Site BS02

Receptor Information
>7n7c Chain A (length=270) Species: 537970 (Helicobacter canadensis MIT 98-5491) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKLCIAGKNNIAVNSLEYILKNHFKPDQVAVIPNKNDFGVDSWQKSLLH
YAFNNHIKVITLEEAYELKQIIFFSLEFDRIVKVEKFKSDKLFNMHFSAL
PKYKGVFTSITPILNNEVESGVTLHCIDNGIDTGNIIDQYIFPININDTA
RDLYFNYLSYGEYLFKKNIQRIINNTYENFKQNNISSSYFSRQDININHK
INFKKTSFEIHNQIRAFIFKEYQLPSINKTKIIKSTLTNEFIGYNMFEEF
EEYFMISGIDGFKIIAQKYN
Ligand information
Ligand IDT3Q
InChIInChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12-,13-,15-/m1/s1
InChIKeyKVYJLJOGNUNRJK-HALQBZCBSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](N)[CH]1O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
CACTVS 3.341C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](N)[C@@H]1O
FormulaC16 H27 N3 O14 P2
Name[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate;
thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose
ChEMBL
DrugBank
ZINCZINC000008436920
PDB chain7n7c Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7n7c Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
K9 E77 F78 V106 F107 T108 S109 Y154 R192 F219 Y222 Q223
Binding residue
(residue number reindexed from 1)
K9 E77 F78 V106 F107 T108 S109 Y154 R192 F219 Y222 Q223
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004479 methionyl-tRNA formyltransferase activity
Biological Process
GO:0006413 translational initiation
GO:0009058 biosynthetic process
GO:0071951 conversion of methionyl-tRNA to N-formyl-methionyl-tRNA

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Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7n7c, PDBe:7n7c, PDBj:7n7c
PDBsum7n7c
PubMed34379357
UniProtC5ZW02

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