Structure of PDB 2vtd Chain A Binding Site BS01

Receptor Information
>2vtd Chain A (length=434) 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
IYENAKVCVVNADDALTMPIRERCVSFGVNMGDYHLNHGETWLRVKGEKV
LNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEV
VLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPL
ARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGD
MVLLSPACASLDQFKNFEQRGNEFARLAKELGSH
Ligand information
Ligand IDLKM
InChIInChI=1S/C23H19FN2O7S/c24-20-9-14(12-25)1-2-17(20)13-33-18-5-3-16-11-19(6-4-15(16)10-18)34(31,32)26-21(23(29)30)7-8-22(27)28/h1-6,9-11,21,26H,7-8,13H2,(H,27,28)(H,29,30)/t21-/m1/s1
InChIKeyIRJUSGUHNFMVCK-OAQYLSRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)N[C@H](CCC(=O)O)C(=O)O
CACTVS 3.341OC(=O)CC[C@@H](N[S](=O)(=O)c1ccc2cc(OCc3ccc(cc3F)C#N)ccc2c1)C(O)=O
ACDLabs 10.04O=C(O)C(NS(=O)(=O)c1ccc3c(c1)ccc(OCc2ccc(C#N)cc2F)c3)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.341OC(=O)CC[CH](N[S](=O)(=O)c1ccc2cc(OCc3ccc(cc3F)C#N)ccc2c1)C(O)=O
FormulaC23 H19 F N2 O7 S
NameN-({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID
ChEMBLCHEMBL457526
DrugBankDB08112
ZINCZINC000040848762
PDB chain2vtd Chain A Residue 1441 [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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PDB2vtd Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		D35 T36 R37 F161 H183 K348 A414 S415 L416 N421 F422 H439
Binding residue
(residue number reindexed from 1)		D35 T36 R37 F161 H183 K343 A409 S410 L411 N416 F417 H434
Annotation score1
Binding affinityMOAD: ic50=85uM
PDBbind-CN: -logKd/Ki=4.07,IC50=85uM
BindingDB: Kd=7000nM,IC50=85000nM
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:2vtd, PDBe:2vtd, PDBj:2vtd
PDBsum2vtd
PubMed19007109
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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