Structure of PDB 1m0o Chain A Binding Site BS01

Receptor Information
>1m0o 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 IDMPM
InChIInChI=1S/C12H20N2O8P2/c1-4-12(3,23(16,17)18)14-6-10-9(7-22-24(19,20)21)5-13-8(2)11(10)15/h5-6,15H,4,7H2,1-3H3,(H2,16,17,18)(H2,19,20,21)/b14-6+/t12-/m1/s1
InChIKeyCFHOMAMSGWRSCJ-CHJAJTDHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC[C](C)(N=Cc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
CACTVS 3.341CC[C@](C)(N=Cc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
OpenEye OEToolkits 1.5.0CCC(C)(N=Cc1c(cnc(c1O)C)COP(=O)(O)O)P(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1/C=N/C(C)(CC)P(=O)(O)O)C
OpenEye OEToolkits 1.5.0CC[C@](C)(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)P(=O)(O)O
FormulaC12 H20 N2 O8 P2
Name(1R)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]-1-METHYLPROPYLPHOSPHONIC ACID
ChEMBL
DrugBank
ZINCZINC000038187910
PDB chain1m0o 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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PDB1m0o Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Q52 G111 A112 W138 H139 E210 D243 Q246 K272 R406
Binding residue
(residue number reindexed from 1)		Q50 G109 A110 W136 H137 E208 D241 Q244 K270 R404
Annotation score1
Binding affinityMOAD: Ki=4.9mM
PDBbind-CN: -logKd/Ki=2.31,Ki=4.9mM
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:1m0o, PDBe:1m0o, PDBj:1m0o
PDBsum1m0o
PubMed12369820
UniProtP16932|DGDA_BURCE 2,2-dialkylglycine decarboxylase (Gene Name=dgdA)

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