Structure of PDB 2y2i Chain A Binding Site BS01

Receptor Information
>2y2i Chain A (length=467) Species: 171101 (Streptococcus pneumoniae R6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISEITYSDGTVIASIDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEAT
QKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVE
VGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIA
IDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPA
YWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGY
QTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLR
EVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLT
LGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDP
SVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFA
IGGSDADYQNAWSSIVG
Ligand information
Ligand IDZA3
InChIInChI=1S/C8H10BN2O6/c12-8(10-5-9(13,14)15)6-3-1-2-4-7(6)11(16)17/h1-4,13-15H,5H2,(H,10,12)/q-1
InChIKeyYKMUZZUWSQWVEH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352O[B-](O)(O)CNC(=O)c1ccccc1[N+]([O-])=O
OpenEye OEToolkits 1.6.1[B-](CNC(=O)c1ccccc1[N+](=O)[O-])(O)(O)O
FormulaC8 H10 B N2 O6
NameTRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON
ChEMBL
DrugBank
ZINCZINC000199226740
PDB chain2y2i Chain A Residue 1000 [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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PDB2y2i Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa).
Resolution1.78 Å
Binding residue
(original residue number in PDB)		A459 S460 K463 S516 N518 M556 G558 T654
Binding residue
(residue number reindexed from 1)		A138 S139 K142 S195 N197 M235 G237 T333
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.59,IC50=26uM
Enzymatic activity
Enzyme Commision number 2.4.1.129: Transferred entry: 2.4.99.28.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding

View graph for
Molecular Function
External links
PDB RCSB:2y2i, PDBe:2y2i, PDBj:2y2i
PDBsum2y2i
PubMed21732689
UniProtQ7CRA4

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