Structure of PDB 1jdj Chain A Binding Site BS01

Receptor Information
>1jdj Chain A (length=346) Species: 5665 (Leishmania mexicana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKR
ENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGN
LIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAI
EVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASA
VKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGL
AGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRAVAEGVATADPLMRL
AKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFK
Ligand information
Ligand IDCFP
InChIInChI=1S/C5H2ClFN4/c6-3-2-4(9-1-8-2)11-5(7)10-3/h1H,(H,8,9,10,11)
InChIKeyUNRIYCIDCQDGQE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1[nH]c2c(n1)c(nc(n2)F)Cl
CACTVS 3.341Fc1nc(Cl)c2nc[nH]c2n1
ACDLabs 10.04Fc2nc1c(ncn1)c(Cl)n2
FormulaC5 H2 Cl F N4
Name6-CHLORO-2-FLUOROPURINE
ChEMBL
DrugBankDB03520
ZINCZINC000006585256
PDB chain1jdj Chain A Residue 367 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1jdj Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		W44 M46 F97
Binding residue
(residue number reindexed from 1)		W36 M38 F89
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.30,IC50=5mM
Enzymatic activity
Catalytic site (original residue number in PDB) K210 T267
Catalytic site (residue number reindexed from 1) K202 T259
Enzyme Commision number 1.1.1.8: glycerol-3-phosphate dehydrogenase (NAD(+)).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006072 glycerol-3-phosphate metabolic process
GO:0006116 NADH oxidation
GO:0046168 glycerol-3-phosphate catabolic process
Cellular Component
GO:0005829 cytosol
GO:0020015 glycosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1jdj, PDBe:1jdj, PDBj:1jdj
PDBsum1jdj
PubMed12445769
UniProtP90551|GPDA_LEIME Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal (Gene Name=GPD)

[Back to BioLiP]