Structure of PDB 2p53 Chain A Binding Site BS02

Receptor Information
>2p53 Chain A (length=382) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAI
LSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLI
TTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRK
PDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATL
KEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGL
HVDYANIRNAKRLKGDKLCLVTNATAPAGANIEQFIFAGKTIYYRNGLCV
DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLG
TLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ
Ligand information
Ligand IDNNG
InChIInChI=1S/C7H17NO10P2/c1-19(12,13)8-4-6(10)5(9)3(18-7(4)11)2-17-20(14,15)16/h3-7,9-11H,2H2,1H3,(H2,8,12,13)(H2,14,15,16)/t3-,4-,5-,6-,7+/m1/s1
InChIKeyYCTZDNRMKSWCHF-GKHCUFPYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCC1OC(O)C(NP(=O)(O)C)C(O)C1O
OpenEye OEToolkits 1.5.0C[P@@](=O)(N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O)COP(=O)(O)O)O)O)O
CACTVS 3.341C[P@@](O)(=O)N[C@H]1[C@@H](O)O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0CP(=O)(NC1C(C(C(OC1O)COP(=O)(O)O)O)O)O
CACTVS 3.341C[P](O)(=O)N[CH]1[CH](O)O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O
FormulaC7 H17 N O10 P2
Name2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-6-O-phosphono-alpha-D-glucopyranose;
N-ACETYLPHOSPHONOAMIDATE-D-GLUCOSAMINE-6-PHOSPHATE;
2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-6-O-phosphono-alpha-D-glucose;
2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-6-O-phosphono-D-glucose;
2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-6-O-phosphono-glucose
ChEMBL
DrugBank
ZINCZINC000016052348
PDB chain2p53 Chain A Residue 411 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2p53 Structural Diversity within the Mononuclear and Binuclear Active Sites of N-Acetyl-d-glucosamine-6-phosphate Deacetylase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		N61 E131 G141 T142 H143 H195 H216 N219 A220 H251 N273 F287 L306 G308
Binding residue
(residue number reindexed from 1)		N61 E131 G141 T142 H143 H195 H216 N219 A220 H251 N273 F287 L306 G308
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=7.46,Ki=35nM
Enzymatic activity
Enzyme Commision number 3.5.1.25: N-acetylglucosamine-6-phosphate deacetylase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008448 N-acetylglucosamine-6-phosphate deacetylase activity
GO:0016787 hydrolase activity
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0047419 N-acetylgalactosamine-6-phosphate deacetylase activity
Biological Process
GO:0006040 amino sugar metabolic process
GO:0006044 N-acetylglucosamine metabolic process
GO:0006046 N-acetylglucosamine catabolic process
GO:0019262 N-acetylneuraminate catabolic process
GO:0051289 protein homotetramerization
Cellular Component
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2p53, PDBe:2p53, PDBj:2p53
PDBsum2p53
PubMed17567048
UniProtP0AF18|NAGA_ECOLI N-acetylglucosamine-6-phosphate deacetylase (Gene Name=nagA)

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