Structure of PDB 4z1d Chain B Binding Site BS02

Receptor Information
>4z1d Chain B (length=256) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSVLIAGPCVIESLENLRSIATKLQPLANNERLDFYFKASFDKANRTSLE
SYRGPGLEKGLEMLQTIKEEFGYKILTDVHESYQASVAAKVADILQIPAF
LCRQTDLIVEVSQTNAIVNIKKGQFMNPKDMQYSVLKALKTRDKSIQSPT
YETALKNGVWLCERGSSFGYGNLVVDMRSLKIMREFAPVIFDATHSVQMP
SFAPILARAAAAVGIDGLFAETHVDPKNALSDGANMLKPDELEQLVTDML
KIQNLF
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4z1d Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4z1d Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).
Resolution1.65 Å
Binding residue
(original residue number in PDB)		C18 H204 E241
Binding residue
(residue number reindexed from 1)		C9 H195 E221
Annotation score1
Enzymatic activity
Enzyme Commision number 2.5.1.55: 3-deoxy-8-phosphooctulonate synthase.
Gene Ontology
Molecular Function
GO:0008676 3-deoxy-8-phosphooctulonate synthase activity
GO:0016740 transferase activity
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4z1d, PDBe:4z1d, PDBj:4z1d
PDBsum4z1d
PubMed26649906
UniProtP56060|KDSA_HELPY 2-dehydro-3-deoxyphosphooctonate aldolase (Gene Name=kdsA)

[Back to BioLiP]