Structure of PDB 1m0n Chain A Binding Site BS01

Receptor Information
>1m0n Chain A (length=431) Species: 292 (Burkholderia cepacia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQ
MSAVLGHCHPEIVSVIGEYAGKLDHLFSEMLSRPVVDLATRLANITPPGL
DRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSA
GRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSG
NLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRT
GTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYT
THVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIG
DVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMG
GVFRIAPPLTVSEDEIDLGLSLLGQAIERAL
Ligand information
Ligand IDHCP
InChIInChI=1S/C13H20N2O8P2/c1-9-12(16)11(10(6-14-9)8-23-25(20,21)22)7-15-13(24(17,18)19)4-2-3-5-13/h6-7,16H,2-5,8H2,1H3,(H2,17,18,19)(H2,20,21,22)/b15-7+
InChIKeyNPYNJFSRGFRPCR-VIZOYTHASA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)C2(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)CCCC2
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2(CCCC2)P(=O)(O)O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=NC2(CCCC2)[P](O)(O)=O)c1O
FormulaC13 H20 N2 O8 P2
Name1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]CYCLOPENTYLPHOSPHONIC ACID
ChEMBL
DrugBank
ZINCZINC000038182187
PDB chain1m0n Chain A Residue 434 [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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PDB1m0n Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Q52 M53 A112 N115 W138 H139 E210 S215 D243 A245 Q246 K272 R406
Binding residue
(residue number reindexed from 1)		Q50 M51 A110 N113 W136 H137 E208 S213 D241 A243 Q244 K270 R404
Annotation score1
Binding affinityMOAD: Ki=6mM
PDBbind-CN: -logKd/Ki=2.22,Ki=6.0mM
Enzymatic activity
Catalytic site (original residue number in PDB) G21 W138 E210 D243 Q246 K272 T303 R406
Catalytic site (residue number reindexed from 1) G19 W136 E208 D241 Q244 K270 T301 R404
Enzyme Commision number 4.1.1.64: 2,2-dialkylglycine decarboxylase (pyruvate).
Gene Ontology
Molecular Function
GO:0008453 alanine-glyoxylate transaminase activity
GO:0008483 transaminase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0047432 2,2-dialkylglycine decarboxylase (pyruvate) activity
Biological Process
GO:0009436 glyoxylate catabolic process
GO:0019481 L-alanine catabolic process, by transamination

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1m0n, PDBe:1m0n, PDBj:1m0n
PDBsum1m0n
PubMed12369820
UniProtP16932|DGDA_BURCE 2,2-dialkylglycine decarboxylase (Gene Name=dgdA)

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