Structure of PDB 6vim Chain H Binding Site BS02

Receptor Information
>6vim Chain H (length=357) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVLITGLRTRAVNVPLAYPVHTAVGTVGTAPLVLIDLATSAGVVGHSYLF
AYTPVALKSLKQLLDDMAAMIVNEPLAPVSLEAMLAKRFCLAGYTGLIRM
AAAGIDMAAWDALGKVHETPLVKLLGANARPVQAYDSHSLDGVKLATERA
VTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDDFGIMVDYNQSLDV
PAAIKRSQALQQEGVTWIEEPTLQHDYEGHQRIQSKLNVPVQMGENWLGP
EEMFKALSIGACRLAMPDAMKIGGVTGWIRASALAQQFGIPMSSHLFQEI
SAHLLAATPTAHWLERLDLAGSVIEPTLTFEGGNAVIPDLPGVGIIWREK
EIGKYLV
Ligand information
Ligand IDPBC
InChIInChI=1S/C6H7BO2/c8-7(9)6-4-2-1-3-5-6/h1-5,8-9H
InChIKeyHXITXNWTGFUOAU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0B(c1ccccc1)(O)O
ACDLabs 10.04
CACTVS 3.341		OB(O)c1ccccc1
FormulaC6 H7 B O2
NamePHENYL BORONIC ACID
ChEMBLCHEMBL21485
DrugBankDB01795
ZINCZINC000169743014
PDB chain6vim Chain H Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vim Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K164 K166 D195 E247 H297 L298 L319
Binding residue
(residue number reindexed from 1)		K162 K164 D193 E245 H295 L296 L317
Annotation score1
Binding affinityMOAD: Ki=1.8uM
Enzymatic activity
Catalytic site (original residue number in PDB) V22 S139 K164 K166 D195 N197 E221 G246 E247 D270 H297 L298 F299 E317
Catalytic site (residue number reindexed from 1) V20 S137 K162 K164 D193 N195 E219 G244 E245 D268 H295 L296 F297 E315
Enzyme Commision number 5.1.2.2: mandelate racemase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016836 hydro-lyase activity
GO:0016853 isomerase activity
GO:0018838 mandelate racemase activity
GO:0046872 metal ion binding
Biological Process
GO:0009063 amino acid catabolic process
GO:0016052 carbohydrate catabolic process
GO:0018924 mandelate metabolic process
GO:0019596 mandelate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vim, PDBe:6vim, PDBj:6vim
PDBsum6vim
PubMed32786399
UniProtP11444|MANR_PSEPU Mandelate racemase (Gene Name=mdlA)

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