Structure of PDB 2rkb Chain D Binding Site BS01

Receptor Information
>2rkb Chain D (length=318) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QEPFHVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQEMA
KKGCRHLVCSSGGNAGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEG
AEVQLTGKVWDEANLRAQELAKRDGWENVPPFDHPLIWKGHASLVQELKA
VLRTPPGALVLAVGGGGLLAGVVAGLLEVGWQHVPIIAMETHGAHCFNAA
ITAGKLVTLPDITSVAKSLGAKTVAARALECMQVCKIHSEVVEDTEAVSA
VQQLLDDERMLVEPACGAALAAIYSGLLRRLQAEGCLPPSLTSVVVIVCG
GNNINSRELQALKTHLGQ
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 chain2rkb Chain D Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2rkb A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		F47 K48 N74 G174 G175 G176 G177 S228 C309
Binding residue
(residue number reindexed from 1)		F37 K38 N64 G164 G165 G166 G167 S218 C299
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K48 G72 E200 A204 C206 S228 A275 C309
Catalytic site (residue number reindexed from 1) K38 G62 E190 A194 C196 S218 A265 C299
Enzyme Commision number 4.3.1.17: L-serine ammonia-lyase.
4.3.1.19: threonine ammonia-lyase.
Gene Ontology
Molecular Function
GO:0003674 molecular_function
GO:0003941 L-serine ammonia-lyase activity
GO:0004794 threonine deaminase activity
GO:0008881 glutamate racemase activity
GO:0016829 lyase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006565 L-serine catabolic process
GO:0006567 threonine catabolic process
GO:0006629 lipid metabolic process
GO:0008150 biological_process
GO:0009097 isoleucine biosynthetic process
Cellular Component
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:2rkb, PDBe:2rkb, PDBj:2rkb
PDBsum2rkb
PubMed18342636
UniProtQ96GA7|SDSL_HUMAN Serine dehydratase-like (Gene Name=SDSL)

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