Structure of PDB 2uup Chain A Binding Site BS01

Receptor Information
>2uup Chain A (length=439) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAV
ERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCR
EAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDE
CELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLR
IYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRV
KGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLP
HRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSA
DFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPR
VQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH
Ligand information
Ligand IDLK4
InChIInChI=1S/C23H20N2O7S/c24-13-15-1-3-16(4-2-15)14-32-19-7-5-18-12-20(8-6-17(18)11-19)33(30,31)25-21(23(28)29)9-10-22(26)27/h1-8,11-12,21,25H,9-10,14H2,(H,26,27)(H,28,29)/t21-/m1/s1
InChIKeyPUHRQSFXADUGJW-OAQYLSRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1COc2ccc3cc(ccc3c2)S(=O)(=O)N[C@H](CCC(=O)O)C(=O)O)C#N
CACTVS 3.341OC(=O)CC[C@@H](N[S](=O)(=O)c1ccc2cc(OCc3ccc(cc3)C#N)ccc2c1)C(O)=O
OpenEye OEToolkits 1.5.0c1cc(ccc1COc2ccc3cc(ccc3c2)S(=O)(=O)NC(CCC(=O)O)C(=O)O)C#N
CACTVS 3.341OC(=O)CC[CH](N[S](=O)(=O)c1ccc2cc(OCc3ccc(cc3)C#N)ccc2c1)C(O)=O
ACDLabs 10.04O=C(O)C(NS(=O)(=O)c1ccc3c(c1)ccc(OCc2ccc(C#N)cc2)c3)CCC(=O)O
FormulaC23 H20 N2 O7 S
NameN-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID
ChEMBLCHEMBL458966
DrugBankDB08108
ZINCZINC000016052548
PDB chain2uup Chain A Residue 1440 [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]
PDB2uup Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme.
Resolution1.88 Å
Binding residue
(original residue number in PDB)		D35 T36 R37 G73 H183 K348 A414 S415 L416 N421 F422 H439
Binding residue
(residue number reindexed from 1)		D35 T36 R37 G73 H183 K348 A414 S415 L416 N421 F422 H439
Annotation score1
Binding affinityMOAD: ic50=105uM
PDBbind-CN: -logKd/Ki=3.98,IC50=105uM
BindingDB: IC50=105000nM
Enzymatic activity
Catalytic site (original residue number in PDB) K115 S116 N138 L147 H183
Catalytic site (residue number reindexed from 1) K115 S116 N138 L147 H183
Enzyme Commision number 6.3.2.9: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0042802 identical protein binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2uup, PDBe:2uup, PDBj:2uup
PDBsum2uup
PubMed19007109
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

[Back to BioLiP]