Structure of PDB 1d7v Chain A Binding Site BS02

Receptor Information
>1d7v 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]
LNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQ
MSAVLGHCHPEIVSVIGEYAGKLDHLFSGMLSRPVVDLATRLANITPPGL
DRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSA
GRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSG
NLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRT
GTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYT
THVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIG
DVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMG
GVFRIAPPLTVSEDEIDLGLSLLGQAIERAL
Ligand information
Ligand IDNMA
InChIInChI=1S/C12H19N2O7P/c1-7-10(15)9(5-14-12(2,3)11(16)17)8(4-13-7)6-21-22(18,19)20/h4,14-15H,5-6H2,1-3H3,(H,16,17)(H2,18,19,20)
InChIKeyNHGDGJKONAZETF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNC(C)(C)C(O)=O)c1O
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)(C)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)(C)C(=O)O)O
FormulaC12 H19 N2 O7 P
NameN-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE;
N-PYRIDOXYL-2-METHYLALANINE-5-PHOSPHATE
ChEMBL
DrugBankDB04241
ZINCZINC000002046989
PDB chain1d7v Chain A Residue 500 [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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PDB1d7v Crystal structures of dialkylglycine decarboxylase inhibitor complexes.
Resolution2.8 Å
Binding residue
(original residue number in PDB)
A112 W138 H139 E210 S215 D243 A245 Q246 K272 R406
Binding residue
(residue number reindexed from 1)
A110 W136 H137 E208 S213 D241 A243 Q244 K270 R404
Annotation score1
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

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Molecular Function

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Biological Process
External links
PDB RCSB:1d7v, PDBe:1d7v, PDBj:1d7v
PDBsum1d7v
PubMed10556038
UniProtP16932|DGDA_BURCE 2,2-dialkylglycine decarboxylase (Gene Name=dgdA)

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