Structure of PDB 2wpb Chain D Binding Site BS01

Receptor Information
>2wpb Chain D (length=295) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEA
FVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFD
AVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQ
INTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDNIFASGLLAG
ADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGV
FRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER
Ligand information
Ligand IDZZI
InChIInChI=1S/C10H21NO4/c1-3-5-11(6-4-2)10(15)9(14)8(13)7-12/h8-9,12-14H,3-7H2,1-2H3/t8-,9-/m1/s1
InChIKeyJYHQCIGUBKFYNN-RKDXNWHRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CCCN(CCC)C(=O)[C@@H]([C@@H](CO)O)O
CACTVS 3.352CCCN(CCC)C(=O)[C@H](O)[C@H](O)CO
CACTVS 3.352CCCN(CCC)C(=O)[CH](O)[CH](O)CO
OpenEye OEToolkits 1.6.1CCCN(CCC)C(=O)C(C(CO)O)O
ACDLabs 10.04O=C(N(CCC)CCC)C(O)C(O)CO
FormulaC10 H21 N O4
Name(2R,3R)-2,3,4-TRIHYDROXY-N,N-DIPROPYLBUTANAMIDE
ChEMBL
DrugBank
ZINCZINC000058650004
PDB chain2wpb Chain D Residue 1297 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2wpb Structural Insights Into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		G189 Y190 D191 G207 S208 I243
Binding residue
(residue number reindexed from 1)		G188 Y189 D190 G206 S207 I242
Annotation score1
Binding affinityMOAD: Ki=1.3mM
PDBbind-CN: -logKd/Ki=2.89,Ki=1.3mM
Enzymatic activity
Catalytic site (original residue number in PDB) S47 Y110 Y137 L142 K165 I206
Catalytic site (residue number reindexed from 1) S46 Y109 Y136 L141 K164 I205
Enzyme Commision number 4.1.3.3: N-acetylneuraminate lyase.
Gene Ontology
Molecular Function
GO:0008747 N-acetylneuraminate lyase activity
GO:0016829 lyase activity
GO:0042802 identical protein binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0019262 N-acetylneuraminate catabolic process
GO:0044010 single-species biofilm formation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2wpb, PDBe:2wpb, PDBj:2wpb
PDBsum2wpb
PubMed20826162
UniProtP0A6L4|NANA_ECOLI N-acetylneuraminate lyase (Gene Name=nanA)

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