Structure of PDB 2y2p Chain A Binding Site BS01

Receptor Information
>2y2p Chain A (length=466) 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
SVVKSEVLKSTGQKPGKVSVEVEVTGSTVTSYWANKSGAPATSYRFAIGG
SDADYQNAWSSIVGSL
Ligand information
Ligand IDZ10
InChIInChI=1S/C15H16BFNO4/c1-10(16(20,21)22)18-15(19)14-12(8-5-9-13(14)17)11-6-3-2-4-7-11/h2-10,20-22H,1H3,(H,18,19)/q-1/t10-/m1/s1
InChIKeyOAGWFGAMTLQXFP-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[C@@H](NC(=O)c1c(F)cccc1c2ccccc2)[B-](O)(O)O
OpenEye OEToolkits 1.6.1[B-](C(C)NC(=O)c1c(cccc1F)c2ccccc2)(O)(O)O
CACTVS 3.352C[CH](NC(=O)c1c(F)cccc1c2ccccc2)[B-](O)(O)O
OpenEye OEToolkits 1.6.1[B-]([C@@H](C)NC(=O)c1c(cccc1F)c2ccccc2)(O)(O)O
FormulaC15 H16 B F N O4
Name[(1S)-1-[(2-fluoro-6-phenyl-phenyl)carbonylamino]ethyl]-trihydroxy-boron
ChEMBL
DrugBank
ZINCZINC000199226852
PDB chain2y2p 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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PDB2y2p Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa).
Resolution1.62 Å
Binding residue
(original residue number in PDB)		S460 Y498 S516 N518 M556 G653 T654 T655 G656 D658
Binding residue
(residue number reindexed from 1)		S139 Y177 S195 N197 M235 G332 T333 T334 G335 D337
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.70,IC50=20uM
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:2y2p, PDBe:2y2p, PDBj:2y2p
PDBsum2y2p
PubMed21732689
UniProtQ7CRA4

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