Structure of PDB 2vvt Chain A Binding Site BS01

Receptor Information
>2vvt Chain A (length=269) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPRGSHMSNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYG
PRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVV
GVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLA
CPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPV
IQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPPHEFYTTGSAKMFEE
IASSWLGIENLKAQQIHLG
Ligand information
Ligand IDI24
InChIInChI=1S/C22H28F2N6O2/c1-2-3-11-32-22-27-20(25-7-8-29-9-12-31-13-10-29)19-21(28-22)30(15-26-19)14-16-17(23)5-4-6-18(16)24/h4-6,15H,2-3,7-14H2,1H3,(H,25,27,28)
InChIKeyUGZWPZWADDDTRN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCOc1nc(NCCN2CCOCC2)c3ncn(Cc4c(F)cccc4F)c3n1
OpenEye OEToolkits 1.5.0CCCCOc1nc(c2c(n1)n(cn2)Cc3c(cccc3F)F)NCCN4CCOCC4
ACDLabs 10.04Fc1cccc(F)c1Cn4cnc3c4nc(OCCCC)nc3NCCN2CCOCC2
FormulaC22 H28 F2 N6 O2
Name2-butoxy-9-(2,6-difluorobenzyl)-N-(2-morpholin-4-ylethyl)-9H-purin-6-amine
ChEMBLCHEMBL515774
DrugBankDB07937
ZINCZINC000040915626
PDB chain2vvt Chain A Residue 1269 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vvt Exploring 9-Benzyl Purines as Inhibitors of Glutamate Racemase (Muri) in Gram-Positive Bacteria.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		V14 V152 E153 N155 H187 L190 I250 W254
Binding residue
(residue number reindexed from 1)		V20 V158 E159 N161 H193 L196 I251 W255
Annotation score1
Binding affinityMOAD: ic50=5.8uM
PDBbind-CN: -logKd/Ki=5.24,IC50=5.8uM
BindingDB: IC50=5800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D11 S12 C74 E153 C185 H187
Catalytic site (residue number reindexed from 1) D17 S18 C80 E159 C191 H193
Enzyme Commision number 5.1.1.3: glutamate racemase.
Gene Ontology
Molecular Function
GO:0008881 glutamate racemase activity
GO:0016853 isomerase activity
GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
GO:0036361 racemase activity, acting on amino acids and derivatives
GO:0042802 identical protein binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vvt, PDBe:2vvt, PDBj:2vvt
PDBsum2vvt
PubMed18614367
UniProtQ836J0|MURI_ENTFA Glutamate racemase (Gene Name=murI)

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