Structure of PDB 2nmp Chain D Binding Site BS02

Receptor Information
>2nmp Chain D (length=390) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFE
YSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIIC
MDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETP
TNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYS
ATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGL
KTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTG
CTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASK
NDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPS
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain2nmp Chain D Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2nmp Structural basis for the inhibition mechanism of human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G90 L91 Y114 D187 T189 S209 K212
Binding residue
(residue number reindexed from 1)		G81 L82 Y105 D178 T180 S200 K203
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R62 Y114 D187 K212
Catalytic site (residue number reindexed from 1) R53 Y105 D178 K203
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:0005515 protein binding
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:0006534 cysteine metabolic process
GO:0006629 lipid metabolic process
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:0030968 endoplasmic reticulum unfolded protein response
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
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2nmp, PDBe:2nmp, PDBj:2nmp
PDBsum2nmp
PubMed19019829
UniProtP32929|CGL_HUMAN Cystathionine gamma-lyase (Gene Name=CTH)

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