Structure of PDB 6nba Chain D Binding Site BS01

Receptor Information
>6nba Chain D (length=389) 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
CTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASV
LKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAH
Ligand information
Ligand IDP1T
InChIInChI=1S/C11H15N2O7P/c1-6-10(14)9(4-13-7(2)11(15)16)8(3-12-6)5-20-21(17,18)19/h3,13-14H,2,4-5H2,1H3,(H,15,16)(H2,17,18,19)
InChIKeyBXUDKFHCAMQSRX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(=C)C(=O)O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNC(=C)C(O)=O)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNC(=C)/C(=O)O)C
FormulaC11 H15 N2 O7 P
Name2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
ChEMBL
DrugBank
ZINCZINC000103552502
PDB chain6nba Chain C Residue 501 [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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PDB6nba S-3-Carboxypropyl-l-cysteine specifically inhibits cystathionine gamma-lyase-dependent hydrogen sulfide synthesis.
Resolution2.495 Å
Binding residue
(original residue number in PDB)		Y60 R62
Binding residue
(residue number reindexed from 1)		Y51 R53
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: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:6nba, PDBe:6nba, PDBj:6nba
PDBsum6nba
PubMed31160338
UniProtP32929|CGL_HUMAN Cystathionine gamma-lyase (Gene Name=CTH)

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