Structure of PDB 3gzd Chain A Binding Site BS01

Receptor Information
>3gzd Chain A (length=397) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARE
SLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHANQTSGAKPHFITSS
VEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVT
IMLANNETGIVMPVPEISQRIKALNQERVAAGLPPILVHTDAAQALGKQR
VDVEDLGVDFLTIVGHKFYGPRIGALYIRGLGEFTPLYPMLFGGGQERNF
RPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFGQKR
IHLNSQFPGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSQP
SPVLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQLED
Ligand information
Ligand IDPLR
InChIInChI=1S/C8H12NO5P/c1-5-7(4-14-15(11,12)13)3-9-6(2)8(5)10/h3,10H,4H2,1-2H3,(H2,11,12,13)
InChIKeyRBCOYOYDYNXAFA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C)C
OpenEye OEToolkits 1.5.0Cc1c(cnc(c1O)C)COP(=O)(O)O
FormulaC8 H12 N O5 P
Name(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE;
4'-DEOXYPYRIDOXINE PHOSPHATE
ChEMBLCHEMBL1235333
DrugBank
ZINCZINC000001656021
PDB chain3gzd Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gzd Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G99 T100 H145 D233 A235 Q236 V256 H258 K259
Binding residue
(residue number reindexed from 1)		G69 T70 H103 D191 A193 Q194 V214 H216 K217
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H145 D233 K259
Catalytic site (residue number reindexed from 1) H103 D191 K217
Enzyme Commision number 4.4.1.16: selenocysteine lyase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0009000 selenocysteine lyase activity
GO:0016597 amino acid binding
GO:0016740 transferase activity
GO:0016829 lyase activity
GO:0042803 protein homodimerization activity
GO:0070279 vitamin B6 binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0016261 selenocysteine catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:1902494 catalytic complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gzd, PDBe:3gzd, PDBj:3gzd
PDBsum3gzd
PubMed22295093
UniProtQ96I15|SCLY_HUMAN Selenocysteine lyase (Gene Name=SCLY)

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