Structure of PDB 8j6n Chain B Binding Site BS01

Receptor Information
>8j6n Chain B (length=390) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFLPSFQHFATQAIHVGQEPEQWSSRAVVLPISLATTFKQDSPGQSSGFV
YSRSGNPTRNCLEKAVAALDGAKHCLTFASGLAATTTITHLLKAGDEVIC
MDEVYGGTNRYFRRVASEFGLKISFVDCSKTKLLEAAITPQTKLVWIETP
TNPTLKLADIKACAQIVHKHKDIILVVDNTFMSAYFQRPLALGADICMCS
ATKYMNGHSDVVMGLVSVNSDDLNERLRFLQNSLGAVPSPFDCYLCCRGL
KTLQIRMEKHFRNGMAVARFLESNPRVEKVIYPGLPSHPQHELAKRQCTG
CPGMVSFYIKGTLQHAQVFLKNIKLFALAESLGGYESLAELPAIMTHASV
PEKDRATLGISDTLIRLSVGLEDEKDLLEDLGQALKAAHP
Ligand information
Ligand IDTVJ
InChIInChI=1S/C10H13N4O7P/c1-5-8(15)7(3-13-14-10(17)9(11)16)6(2-12-5)4-21-22(18,19)20/h2-3,15H,4H2,1H3,(H2,11,16)(H,14,17)(H2,18,19,20)/b13-3+
InChIKeyQXOGMDGTZNDNSY-QLKAYGNNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/NC(=O)C(=O)N)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(\C=N\NC(=O)C(N)=O)c1O
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)C=NNC(=O)C(=O)N)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=NNC(=O)C(N)=O)c1O
FormulaC10 H13 N4 O7 P
Name[6-methyl-4-[(~{E})-(oxamoylhydrazinylidene)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8j6n Chain B Residue 401 [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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PDB8j6n Discovery of a cystathionine gamma-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G90 L91 Y114 E157 N161 D187 S209 T211 K212 E339 S340 T355 R375
Binding residue
(residue number reindexed from 1)		G81 L82 Y105 E148 N152 D178 S200 T202 K203 E330 S331 T346 R366
Annotation score1
Enzymatic activity
Enzyme Commision number 4.4.1.1: cystathionine gamma-lyase.
4.4.1.2: homocysteine desulfhydrase.
Gene Ontology
Molecular Function
GO:0004123 cystathionine gamma-lyase activity
GO:0005516 calmodulin binding
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
GO:0044540 L-cystine L-cysteine-lyase (deaminating)
GO:0047982 homocysteine desulfhydrase activity
GO:0080146 L-cysteine desulfhydrase activity
GO:0098606 selenocystathionine gamma-lyase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0006749 glutathione metabolic process
GO:0008285 negative regulation of cell population proliferation
GO:0018272 protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine
GO:0019343 cysteine biosynthetic process via cystathionine
GO:0019344 cysteine biosynthetic process
GO:0019346 transsulfuration
GO:0030308 negative regulation of cell growth
GO:0043066 negative regulation of apoptotic process
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0044524 protein sulfhydration
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0051289 protein homotetramerization
GO:0070814 hydrogen sulfide biosynthetic process
GO:1904831 positive regulation of aortic smooth muscle cell differentiation
GO:1990830 cellular response to leukemia inhibitory factor
GO:2001234 negative regulation of apoptotic signaling pathway
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8j6n, PDBe:8j6n, PDBj:8j6n
PDBsum8j6n
PubMed37777556
UniProtP18757|CGL_RAT Cystathionine gamma-lyase (Gene Name=Cth)

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